Starting phenix.real_space_refine on Wed Mar 20 03:07:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fwk_3337/03_2024/5fwk_3337_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fwk_3337/03_2024/5fwk_3337.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/5fwk_3337/03_2024/5fwk_3337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fwk_3337/03_2024/5fwk_3337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fwk_3337/03_2024/5fwk_3337_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fwk_3337/03_2024/5fwk_3337_trim_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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 8284 2.51 5 N 2227 2.21 5 O 2530 1.98 5 H 13109 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26221 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 10400 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 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: 10243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 10243 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 17, 'TRANS': 613} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2170 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3344 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 19, 'TRANS': 190} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.87, per 1000 atoms: 0.45 Number of scatterers: 26221 At special positions: 0 Unit cell: (99.94, 145.965, 134.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 62 16.00 P 7 15.00 Mg 2 11.99 O 2530 8.00 N 2227 7.00 C 8284 6.00 H 13109 1.00 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: 22.04 Conformation dependent library (CDL) restraints added in 2.8 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 10 sheets defined 43.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 removed outlier: 4.029A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 60 removed outlier: 3.687A pdb=" N GLU A 42 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 58 " --> pdb=" O ARG A 55 " (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 110 through 116 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 195 through 204 removed outlier: 3.679A pdb=" N LYS A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.824A pdb=" N GLU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 369 No H-bonds generated for 'chain 'A' and resid 366 through 369' 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 Processing helix chain 'A' and resid 423 through 443 removed outlier: 5.723A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 removed outlier: 4.891A pdb=" N GLU A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 491 through 496 Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.938A pdb=" N ARG A 502 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 503 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.914A pdb=" N GLN A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 561 through 570 Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.633A pdb=" N ALA A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 633 through 644 Processing helix chain 'A' and resid 649 through 666 Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 21 through 28 removed outlier: 4.309A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.543A pdb=" N GLU B 42 " --> pdb=" O PHE B 39 " (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 119 removed outlier: 4.969A pdb=" N ALA B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 280 through 283 removed outlier: 4.337A pdb=" N ASN B 283 " --> pdb=" O GLU B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 366 through 369 No H-bonds generated for 'chain 'B' and resid 366 through 369' 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 Processing helix chain 'B' and resid 423 through 443 removed outlier: 4.230A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.533A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 3.915A 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 498 through 505 removed outlier: 4.939A pdb=" N ARG B 502 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 503 " --> pdb=" O VAL B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 4.237A pdb=" N VAL B 522 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 523 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 Processing helix chain 'B' and resid 561 through 570 Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 633 through 645 Processing helix chain 'B' and resid 649 through 665 Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'E' and resid 5 through 7 No H-bonds generated for 'chain 'E' and resid 5 through 7' Processing helix chain 'E' and resid 25 through 73 removed outlier: 4.694A pdb=" N ARG E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 111 removed outlier: 3.547A pdb=" N ARG E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 106 Processing helix chain 'K' and resid 114 through 133 Processing helix chain 'K' and resid 143 through 145 No H-bonds generated for 'chain 'K' and resid 143 through 145' Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 183 through 186 No H-bonds generated for 'chain 'K' and resid 183 through 186' Processing helix chain 'K' and resid 193 through 209 Processing helix chain 'K' and resid 219 through 230 removed outlier: 4.217A pdb=" N ASP K 228 " --> pdb=" O GLY K 224 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU K 229 " --> pdb=" O LYS K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 260 No H-bonds generated for 'chain 'K' and resid 257 through 260' Processing helix chain 'K' and resid 266 through 276 Processing helix chain 'K' and resid 286 through 290 Processing sheet with id= A, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.850A pdb=" N ILE A 73 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR A 216 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 75 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N GLU A 218 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 317 through 323 removed outlier: 6.100A pdb=" N VAL A 357 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 456 through 458 Processing sheet with id= D, first strand: chain 'A' and resid 533 through 535 removed outlier: 6.051A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 578 through 580 removed outlier: 6.321A pdb=" N LEU A 626 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 275 through 279 removed outlier: 6.835A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N TYR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 75 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 178 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 317 through 323 removed outlier: 6.312A pdb=" N VAL B 357 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE B 361 " --> pdb=" O VAL B 357 " (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 removed outlier: 3.545A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 146 through 148 557 hydrogen bonds defined for protein. 1308 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: 10.08 Time building geometry restraints manager: 22.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 13091 1.13 - 1.30: 2264 1.30 - 1.47: 4961 1.47 - 1.64: 6031 1.64 - 1.81: 106 Bond restraints: 26453 Sorted by residual: bond pdb=" CE1 HIS B 632 " pdb=" HE1 HIS B 632 " ideal model delta sigma weight residual 0.930 1.104 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" CD2 HIS B 632 " pdb=" HD2 HIS B 632 " ideal model delta sigma weight residual 0.930 1.098 -0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" N ASP A 311 " pdb=" H ASP A 311 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C4 ATP A 725 " pdb=" C5 ATP A 725 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" CD2 HIS A 632 " pdb=" HD2 HIS A 632 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.89e+01 ... (remaining 26448 not shown) Histogram of bond angle deviations from ideal: 95.74 - 103.73: 155 103.73 - 111.71: 30215 111.71 - 119.69: 8217 119.69 - 127.68: 9245 127.68 - 135.66: 121 Bond angle restraints: 47953 Sorted by residual: angle pdb=" PB ATP A 725 " pdb=" O3B ATP A 725 " pdb=" PG ATP A 725 " ideal model delta sigma weight residual 139.87 112.14 27.73 1.00e+00 1.00e+00 7.69e+02 angle pdb=" PB ATP B 725 " pdb=" O3B ATP B 725 " pdb=" PG ATP B 725 " ideal model delta sigma weight residual 139.87 114.43 25.44 1.00e+00 1.00e+00 6.47e+02 angle pdb=" PA ATP B 725 " pdb=" O3A ATP B 725 " pdb=" PB ATP B 725 " ideal model delta sigma weight residual 136.83 112.04 24.79 1.00e+00 1.00e+00 6.15e+02 angle pdb=" PA ATP A 725 " pdb=" O3A ATP A 725 " pdb=" PB ATP A 725 " ideal model delta sigma weight residual 136.83 114.69 22.14 1.00e+00 1.00e+00 4.90e+02 angle pdb=" C ASN B 78 " pdb=" N PRO B 79 " pdb=" CA PRO B 79 " ideal model delta sigma weight residual 119.56 129.61 -10.05 1.02e+00 9.61e-01 9.70e+01 ... (remaining 47948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 11648 17.88 - 35.75: 303 35.75 - 53.63: 137 53.63 - 71.50: 245 71.50 - 89.37: 7 Dihedral angle restraints: 12340 sinusoidal: 6885 harmonic: 5455 Sorted by residual: dihedral pdb=" CD2 HIS A 458 " pdb=" CG HIS A 458 " pdb=" ND1 HIS A 458 " pdb=" HD1 HIS A 458 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CD2 HIS B 315 " pdb=" CG HIS B 315 " pdb=" ND1 HIS B 315 " pdb=" HD1 HIS B 315 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CD2 HIS B 632 " pdb=" CG HIS B 632 " pdb=" ND1 HIS B 632 " pdb=" HD1 HIS B 632 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 12337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1041 0.052 - 0.103: 652 0.103 - 0.155: 227 0.155 - 0.206: 53 0.206 - 0.258: 6 Chirality restraints: 1979 Sorted by residual: chirality pdb=" CA ASN B 425 " pdb=" N ASN B 425 " pdb=" C ASN B 425 " pdb=" CB ASN B 425 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA PHE B 659 " pdb=" N PHE B 659 " pdb=" C PHE B 659 " pdb=" CB PHE B 659 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA LYS B 36 " pdb=" N LYS B 36 " pdb=" C LYS B 36 " pdb=" CB LYS B 36 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1976 not shown) Planarity restraints: 3847 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 46 " -0.293 2.00e-02 2.50e+03 3.71e-01 2.07e+03 pdb=" CG ASN B 46 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN B 46 " 0.363 2.00e-02 2.50e+03 pdb=" ND2 ASN B 46 " -0.083 2.00e-02 2.50e+03 pdb="HD21 ASN B 46 " 0.579 2.00e-02 2.50e+03 pdb="HD22 ASN B 46 " -0.513 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 46 " -0.231 2.00e-02 2.50e+03 2.27e-01 7.74e+02 pdb=" CG ASN A 46 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 46 " 0.218 2.00e-02 2.50e+03 pdb=" ND2 ASN A 46 " -0.007 2.00e-02 2.50e+03 pdb="HD21 ASN A 46 " 0.321 2.00e-02 2.50e+03 pdb="HD22 ASN A 46 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 458 " -0.072 2.00e-02 2.50e+03 7.58e-02 1.29e+02 pdb=" CG HIS A 458 " -0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS A 458 " -0.071 2.00e-02 2.50e+03 pdb=" CD2 HIS A 458 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS A 458 " -0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 458 " 0.024 2.00e-02 2.50e+03 pdb=" HD1 HIS A 458 " 0.175 2.00e-02 2.50e+03 pdb=" HD2 HIS A 458 " 0.060 2.00e-02 2.50e+03 pdb=" HE1 HIS A 458 " -0.058 2.00e-02 2.50e+03 ... (remaining 3844 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.86: 388 1.86 - 2.54: 25452 2.54 - 3.23: 84474 3.23 - 3.91: 105651 3.91 - 4.60: 166801 Nonbonded interactions: 382766 Sorted by model distance: nonbonded pdb=" OD1 ASN A 46 " pdb="MG MG A 726 " model vdw 1.173 2.050 nonbonded pdb=" HB2 GLN B 609 " pdb=" HG3 ARG B 612 " model vdw 1.204 2.440 nonbonded pdb=" OD1 ASN B 46 " pdb="MG MG B 726 " model vdw 1.316 2.050 nonbonded pdb=" OE1 GLN A 80 " pdb=" H GLN A 80 " model vdw 1.471 1.850 nonbonded pdb=" OE1 GLU B 299 " pdb=" H GLU B 299 " model vdw 1.483 1.850 ... (remaining 382761 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 10 through 220 or resid 273 through 691 or resid 725 throu \ gh 726)) selection = (chain 'B' and (resid 10 through 690 or (resid 691 and (name N )) or resid 725 t \ hrough 726)) } 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: 1.060 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: 0.340 Extract box with map and model: 4.830 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 86.120 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.016 0.113 13344 Z= 1.023 Angle : 1.315 27.726 17970 Z= 0.951 Chirality : 0.071 0.258 1979 Planarity : 0.011 0.153 2301 Dihedral : 10.313 89.375 5213 Min Nonbonded Distance : 1.173 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.95 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: -0.44 (0.20), residues: 1593 helix: -0.21 (0.17), residues: 675 sheet: 0.04 (0.36), residues: 208 loop : -0.29 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.009 TRP E 31 HIS 0.008 0.002 HIS B 632 PHE 0.039 0.006 PHE A 329 TYR 0.044 0.007 TYR A 192 ARG 0.009 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7045 (t0) cc_final: 0.6320 (m-30) REVERT: A 275 LYS cc_start: 0.9189 (mttt) cc_final: 0.8560 (mmmt) REVERT: A 276 TYR cc_start: 0.7713 (m-80) cc_final: 0.7221 (p90) REVERT: A 563 LEU cc_start: 0.7795 (tp) cc_final: 0.7337 (tp) REVERT: A 567 MET cc_start: 0.8793 (mtp) cc_final: 0.8086 (mtp) REVERT: A 606 MET cc_start: 0.8266 (mmm) cc_final: 0.7787 (mmm) REVERT: A 609 GLN cc_start: 0.7934 (tt0) cc_final: 0.6663 (tm-30) REVERT: A 683 MET cc_start: 0.9004 (mmm) cc_final: 0.8752 (mmm) REVERT: B 305 TYR cc_start: 0.8130 (t80) cc_final: 0.7655 (t80) REVERT: B 323 VAL cc_start: 0.9163 (m) cc_final: 0.8764 (m) REVERT: B 363 MET cc_start: 0.7230 (ptp) cc_final: 0.6829 (ptp) REVERT: B 565 LYS cc_start: 0.8864 (mttt) cc_final: 0.8603 (ttpt) REVERT: B 593 THR cc_start: 0.8259 (m) cc_final: 0.7776 (p) REVERT: B 602 MET cc_start: 0.8125 (tpp) cc_final: 0.7831 (tpp) REVERT: E 14 ASP cc_start: 0.8259 (p0) cc_final: 0.7944 (p0) REVERT: E 34 GLN cc_start: 0.8252 (tp40) cc_final: 0.7896 (tp40) REVERT: E 51 ASP cc_start: 0.7290 (t70) cc_final: 0.7040 (t0) REVERT: K 210 ARG cc_start: 0.6642 (ttp-170) cc_final: 0.6260 (ttp80) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.6697 time to fit residues: 402.1660 Evaluate side-chains 265 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 397 GLN B 523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13344 Z= 0.214 Angle : 0.567 5.560 17970 Z= 0.318 Chirality : 0.040 0.177 1979 Planarity : 0.006 0.055 2301 Dihedral : 7.578 88.690 1815 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.92 % Rotamer: Outliers : 1.04 % Allowed : 8.29 % Favored : 90.68 % 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: 0.16 (0.21), residues: 1593 helix: 0.55 (0.19), residues: 674 sheet: 0.02 (0.34), residues: 212 loop : -0.15 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 31 HIS 0.009 0.001 HIS B 632 PHE 0.016 0.002 PHE A 329 TYR 0.017 0.002 TYR A 426 ARG 0.009 0.001 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 296 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 88 ASP cc_start: 0.7271 (t0) cc_final: 0.6526 (m-30) REVERT: A 275 LYS cc_start: 0.9150 (mttt) cc_final: 0.8594 (mmmt) REVERT: A 276 TYR cc_start: 0.7762 (m-80) cc_final: 0.7190 (p90) REVERT: A 500 VAL cc_start: 0.8613 (p) cc_final: 0.8406 (p) REVERT: A 563 LEU cc_start: 0.7705 (tp) cc_final: 0.7104 (tp) REVERT: A 567 MET cc_start: 0.8712 (mtp) cc_final: 0.7910 (mtp) REVERT: A 606 MET cc_start: 0.8406 (mmm) cc_final: 0.8118 (mmm) REVERT: A 609 GLN cc_start: 0.7834 (tt0) cc_final: 0.6734 (pp30) REVERT: B 49 ASP cc_start: 0.7915 (m-30) cc_final: 0.7501 (m-30) REVERT: B 102 LEU cc_start: 0.9372 (tp) cc_final: 0.9114 (mt) REVERT: B 552 LYS cc_start: 0.8632 (mttt) cc_final: 0.8305 (ttpp) REVERT: B 593 THR cc_start: 0.8540 (m) cc_final: 0.8024 (p) REVERT: B 602 MET cc_start: 0.8225 (tpp) cc_final: 0.7878 (tpp) REVERT: B 672 ASP cc_start: 0.7887 (t0) cc_final: 0.7649 (m-30) REVERT: E 14 ASP cc_start: 0.8287 (p0) cc_final: 0.8016 (p0) REVERT: E 46 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7597 (tm-30) REVERT: K 210 ARG cc_start: 0.6580 (ttp-170) cc_final: 0.6186 (ttp80) outliers start: 15 outliers final: 11 residues processed: 303 average time/residue: 0.5664 time to fit residues: 246.7995 Evaluate side-chains 239 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 228 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain E residue 3 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 145 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13344 Z= 0.169 Angle : 0.512 5.409 17970 Z= 0.282 Chirality : 0.040 0.181 1979 Planarity : 0.005 0.050 2301 Dihedral : 7.031 81.798 1815 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.62 % Allowed : 11.33 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1593 helix: 0.48 (0.20), residues: 684 sheet: -0.11 (0.33), residues: 218 loop : -0.09 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 31 HIS 0.004 0.001 HIS B 632 PHE 0.013 0.001 PHE A 429 TYR 0.016 0.001 TYR A 137 ARG 0.005 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 243 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7414 (t0) cc_final: 0.6738 (m-30) REVERT: A 275 LYS cc_start: 0.9116 (mttt) cc_final: 0.8596 (mmtt) REVERT: A 276 TYR cc_start: 0.7749 (m-80) cc_final: 0.7070 (p90) REVERT: A 385 ASP cc_start: 0.7766 (m-30) cc_final: 0.6937 (m-30) REVERT: A 563 LEU cc_start: 0.7925 (tp) cc_final: 0.7447 (tp) REVERT: A 567 MET cc_start: 0.8654 (mtp) cc_final: 0.8001 (mtp) REVERT: A 576 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6922 (mt-10) REVERT: A 606 MET cc_start: 0.8567 (mmm) cc_final: 0.8257 (mmm) REVERT: A 609 GLN cc_start: 0.7981 (tt0) cc_final: 0.6655 (pp30) REVERT: B 102 LEU cc_start: 0.9392 (tp) cc_final: 0.9113 (mt) REVERT: B 512 TYR cc_start: 0.8413 (m-80) cc_final: 0.8081 (m-80) REVERT: B 552 LYS cc_start: 0.8709 (mttt) cc_final: 0.8238 (ttpp) REVERT: B 602 MET cc_start: 0.8376 (tpp) cc_final: 0.7966 (tpp) REVERT: B 672 ASP cc_start: 0.7743 (t0) cc_final: 0.7394 (m-30) REVERT: E 14 ASP cc_start: 0.8120 (p0) cc_final: 0.7797 (p0) REVERT: E 43 PHE cc_start: 0.8682 (t80) cc_final: 0.8438 (t80) REVERT: E 46 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7941 (tm-30) REVERT: E 128 MET cc_start: 0.7907 (tpp) cc_final: 0.7625 (mmt) REVERT: K 144 GLU cc_start: 0.8250 (mp0) cc_final: 0.7497 (tm-30) REVERT: K 210 ARG cc_start: 0.6338 (ttp-170) cc_final: 0.5997 (ttp80) outliers start: 9 outliers final: 7 residues processed: 244 average time/residue: 0.5476 time to fit residues: 197.6185 Evaluate side-chains 224 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 217 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain E residue 3 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13344 Z= 0.258 Angle : 0.543 6.205 17970 Z= 0.299 Chirality : 0.039 0.151 1979 Planarity : 0.004 0.043 2301 Dihedral : 6.969 77.177 1815 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.17 % Allowed : 10.98 % Favored : 87.85 % 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: -0.13 (0.21), residues: 1593 helix: 0.39 (0.20), residues: 681 sheet: -0.27 (0.32), residues: 217 loop : -0.35 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 31 HIS 0.006 0.001 HIS B 632 PHE 0.015 0.002 PHE K 124 TYR 0.017 0.002 TYR B 457 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 226 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LYS cc_start: 0.9137 (mttt) cc_final: 0.8908 (mmtt) REVERT: A 326 GLN cc_start: 0.8620 (tp40) cc_final: 0.8413 (tp-100) REVERT: A 563 LEU cc_start: 0.8019 (tp) cc_final: 0.7430 (tp) REVERT: A 567 MET cc_start: 0.8675 (mtp) cc_final: 0.7966 (mtp) REVERT: A 606 MET cc_start: 0.8688 (mmm) cc_final: 0.8351 (mmm) REVERT: A 625 HIS cc_start: 0.7777 (m-70) cc_final: 0.7471 (m-70) REVERT: B 102 LEU cc_start: 0.9451 (tp) cc_final: 0.9138 (tp) REVERT: B 512 TYR cc_start: 0.8675 (m-80) cc_final: 0.8386 (m-80) REVERT: B 552 LYS cc_start: 0.8724 (mttt) cc_final: 0.8335 (ttpp) REVERT: B 672 ASP cc_start: 0.7866 (t0) cc_final: 0.7657 (m-30) REVERT: E 14 ASP cc_start: 0.8235 (p0) cc_final: 0.7717 (p0) REVERT: E 46 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8143 (tm-30) REVERT: E 128 MET cc_start: 0.7946 (tpp) cc_final: 0.7688 (mmt) REVERT: K 142 LYS cc_start: 0.7164 (pttt) cc_final: 0.6709 (ptpp) REVERT: K 144 GLU cc_start: 0.8270 (mp0) cc_final: 0.7612 (tm-30) REVERT: K 210 ARG cc_start: 0.6305 (ttp-170) cc_final: 0.6049 (ttp80) outliers start: 17 outliers final: 14 residues processed: 232 average time/residue: 0.5330 time to fit residues: 181.6818 Evaluate side-chains 215 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 13344 Z= 0.336 Angle : 0.588 6.830 17970 Z= 0.324 Chirality : 0.040 0.151 1979 Planarity : 0.005 0.041 2301 Dihedral : 7.266 78.996 1815 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.14 % Allowed : 11.19 % Favored : 86.67 % 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: -0.44 (0.20), residues: 1593 helix: 0.26 (0.20), residues: 673 sheet: -0.43 (0.32), residues: 212 loop : -0.66 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 31 HIS 0.005 0.002 HIS B 632 PHE 0.019 0.002 PHE B 113 TYR 0.017 0.002 TYR A 426 ARG 0.006 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LYS cc_start: 0.9126 (mttt) cc_final: 0.8920 (mttm) REVERT: A 326 GLN cc_start: 0.8721 (tp40) cc_final: 0.8480 (tp-100) REVERT: A 563 LEU cc_start: 0.8236 (tp) cc_final: 0.7764 (tp) REVERT: A 567 MET cc_start: 0.8679 (mtp) cc_final: 0.7997 (mtp) REVERT: A 606 MET cc_start: 0.8694 (mmm) cc_final: 0.8409 (mmm) REVERT: A 625 HIS cc_start: 0.7818 (m-70) cc_final: 0.7555 (m-70) REVERT: B 552 LYS cc_start: 0.8732 (mttt) cc_final: 0.8341 (ttpp) REVERT: E 14 ASP cc_start: 0.8300 (p0) cc_final: 0.7940 (p0) REVERT: E 46 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8196 (tm-30) REVERT: K 142 LYS cc_start: 0.7138 (pttt) cc_final: 0.6638 (ptpp) REVERT: K 144 GLU cc_start: 0.8242 (mp0) cc_final: 0.7811 (tm-30) REVERT: K 210 ARG cc_start: 0.6203 (ttp-170) cc_final: 0.5949 (ttp80) outliers start: 31 outliers final: 24 residues processed: 228 average time/residue: 0.4987 time to fit residues: 170.2127 Evaluate side-chains 214 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain E residue 3 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 0.0570 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13344 Z= 0.184 Angle : 0.519 6.491 17970 Z= 0.277 Chirality : 0.039 0.171 1979 Planarity : 0.004 0.039 2301 Dihedral : 6.820 71.310 1815 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.31 % Allowed : 12.43 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1593 helix: 0.48 (0.20), residues: 679 sheet: -0.47 (0.32), residues: 212 loop : -0.54 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 31 HIS 0.004 0.001 HIS B 632 PHE 0.021 0.001 PHE A 321 TYR 0.012 0.001 TYR A 426 ARG 0.004 0.000 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8380 (t0) cc_final: 0.8170 (t0) REVERT: A 275 LYS cc_start: 0.9061 (mttt) cc_final: 0.8828 (mttm) REVERT: A 301 TYR cc_start: 0.6769 (t80) cc_final: 0.6377 (t80) REVERT: A 326 GLN cc_start: 0.8680 (tp40) cc_final: 0.8438 (tp-100) REVERT: A 563 LEU cc_start: 0.8212 (tp) cc_final: 0.7620 (tp) REVERT: A 567 MET cc_start: 0.8649 (mtp) cc_final: 0.7959 (mtp) REVERT: A 606 MET cc_start: 0.8725 (mmm) cc_final: 0.8424 (mmm) REVERT: A 625 HIS cc_start: 0.7719 (m-70) cc_final: 0.7459 (m-70) REVERT: B 125 MET cc_start: 0.8064 (mmm) cc_final: 0.7742 (mmp) REVERT: B 552 LYS cc_start: 0.8699 (mttt) cc_final: 0.8317 (ttpp) REVERT: B 567 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8408 (mtp) REVERT: B 602 MET cc_start: 0.8642 (tpp) cc_final: 0.8279 (tpp) REVERT: E 46 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8173 (tm-30) REVERT: K 142 LYS cc_start: 0.7179 (pttt) cc_final: 0.6663 (ptpp) REVERT: K 144 GLU cc_start: 0.8232 (mp0) cc_final: 0.7910 (tm-30) REVERT: K 210 ARG cc_start: 0.5789 (ttp-170) cc_final: 0.5507 (ttp80) outliers start: 19 outliers final: 16 residues processed: 219 average time/residue: 0.5292 time to fit residues: 176.6456 Evaluate side-chains 213 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain K residue 259 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 0.0030 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN B 279 GLN ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13344 Z= 0.164 Angle : 0.505 9.774 17970 Z= 0.268 Chirality : 0.039 0.172 1979 Planarity : 0.004 0.037 2301 Dihedral : 6.628 69.322 1815 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.17 % Allowed : 12.78 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1593 helix: 0.65 (0.21), residues: 672 sheet: -0.44 (0.32), residues: 212 loop : -0.45 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 31 HIS 0.005 0.001 HIS K 138 PHE 0.014 0.001 PHE B 433 TYR 0.011 0.001 TYR A 426 ARG 0.003 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 35 ASN cc_start: 0.8481 (t0) cc_final: 0.8277 (t0) REVERT: A 301 TYR cc_start: 0.6620 (t80) cc_final: 0.6297 (t80) REVERT: A 326 GLN cc_start: 0.8676 (tp40) cc_final: 0.8434 (tp-100) REVERT: A 563 LEU cc_start: 0.8194 (tp) cc_final: 0.7601 (tp) REVERT: A 567 MET cc_start: 0.8635 (mtp) cc_final: 0.7945 (mtp) REVERT: A 606 MET cc_start: 0.8690 (mmm) cc_final: 0.8436 (mmm) REVERT: A 609 GLN cc_start: 0.7025 (tt0) cc_final: 0.6482 (tm-30) REVERT: A 625 HIS cc_start: 0.7721 (m-70) cc_final: 0.7438 (m-70) REVERT: B 125 MET cc_start: 0.8263 (mmm) cc_final: 0.7827 (mmp) REVERT: B 519 GLU cc_start: 0.8686 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 602 MET cc_start: 0.8627 (tpp) cc_final: 0.8111 (tpp) REVERT: B 605 ILE cc_start: 0.9260 (mt) cc_final: 0.8901 (tp) REVERT: E 46 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8198 (tm-30) REVERT: K 142 LYS cc_start: 0.7168 (pttt) cc_final: 0.6643 (ptpp) REVERT: K 144 GLU cc_start: 0.8223 (mp0) cc_final: 0.7912 (tm-30) REVERT: K 197 MET cc_start: 0.4832 (tpt) cc_final: 0.4558 (tpp) REVERT: K 210 ARG cc_start: 0.5784 (ttp-170) cc_final: 0.5494 (ttp80) outliers start: 17 outliers final: 14 residues processed: 214 average time/residue: 0.4963 time to fit residues: 160.0978 Evaluate side-chains 209 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain K residue 259 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13344 Z= 0.167 Angle : 0.503 11.153 17970 Z= 0.265 Chirality : 0.039 0.168 1979 Planarity : 0.004 0.036 2301 Dihedral : 6.493 68.442 1815 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.90 % Allowed : 13.12 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1593 helix: 0.75 (0.21), residues: 671 sheet: -0.36 (0.33), residues: 210 loop : -0.38 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 31 HIS 0.004 0.001 HIS K 138 PHE 0.014 0.001 PHE B 433 TYR 0.015 0.001 TYR A 457 ARG 0.003 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 205 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LYS cc_start: 0.9010 (mttt) cc_final: 0.8706 (mmmt) REVERT: A 301 TYR cc_start: 0.6580 (t80) cc_final: 0.6235 (t80) REVERT: A 326 GLN cc_start: 0.8665 (tp40) cc_final: 0.8394 (tp-100) REVERT: A 563 LEU cc_start: 0.8195 (tp) cc_final: 0.7604 (tp) REVERT: A 567 MET cc_start: 0.8650 (mtp) cc_final: 0.7980 (mtp) REVERT: A 606 MET cc_start: 0.8730 (mmm) cc_final: 0.8432 (mmm) REVERT: A 625 HIS cc_start: 0.7747 (m-70) cc_final: 0.7442 (m-70) REVERT: B 125 MET cc_start: 0.8263 (mmm) cc_final: 0.7829 (mmp) REVERT: B 519 GLU cc_start: 0.8739 (mm-30) cc_final: 0.7989 (mm-30) REVERT: E 46 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8187 (tm-30) REVERT: K 142 LYS cc_start: 0.7155 (pttt) cc_final: 0.6647 (ptpp) REVERT: K 144 GLU cc_start: 0.8264 (mp0) cc_final: 0.7994 (tm-30) REVERT: K 210 ARG cc_start: 0.5770 (ttp-170) cc_final: 0.5477 (ttp80) outliers start: 13 outliers final: 13 residues processed: 212 average time/residue: 0.5135 time to fit residues: 162.7771 Evaluate side-chains 204 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13344 Z= 0.266 Angle : 0.551 11.176 17970 Z= 0.295 Chirality : 0.039 0.166 1979 Planarity : 0.004 0.037 2301 Dihedral : 6.790 70.700 1815 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.17 % Allowed : 13.47 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1593 helix: 0.51 (0.20), residues: 681 sheet: -0.46 (0.33), residues: 216 loop : -0.51 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 31 HIS 0.005 0.001 HIS A 315 PHE 0.016 0.002 PHE K 124 TYR 0.015 0.002 TYR A 426 ARG 0.004 0.000 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LYS cc_start: 0.9081 (mttt) cc_final: 0.8652 (mttm) REVERT: A 301 TYR cc_start: 0.6776 (t80) cc_final: 0.6297 (t80) REVERT: A 326 GLN cc_start: 0.8677 (tp40) cc_final: 0.8403 (tp-100) REVERT: A 563 LEU cc_start: 0.8315 (tp) cc_final: 0.7534 (tp) REVERT: A 567 MET cc_start: 0.8667 (mtp) cc_final: 0.7885 (mtp) REVERT: A 606 MET cc_start: 0.8704 (mmm) cc_final: 0.8440 (mmm) REVERT: A 625 HIS cc_start: 0.7783 (m-70) cc_final: 0.7464 (m-70) REVERT: B 60 THR cc_start: 0.8281 (p) cc_final: 0.8038 (t) REVERT: E 46 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8217 (tm-30) REVERT: K 142 LYS cc_start: 0.7247 (pttt) cc_final: 0.6690 (ptpp) REVERT: K 210 ARG cc_start: 0.5803 (ttp-170) cc_final: 0.5542 (ttp80) outliers start: 17 outliers final: 15 residues processed: 204 average time/residue: 0.5032 time to fit residues: 154.6126 Evaluate side-chains 201 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain K residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13344 Z= 0.196 Angle : 0.530 12.930 17970 Z= 0.278 Chirality : 0.039 0.163 1979 Planarity : 0.004 0.039 2301 Dihedral : 6.627 71.646 1815 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.97 % Allowed : 13.81 % Favored : 85.22 % 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: -0.05 (0.21), residues: 1593 helix: 0.65 (0.21), residues: 675 sheet: -0.42 (0.33), residues: 214 loop : -0.45 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 157 HIS 0.005 0.001 HIS A 315 PHE 0.014 0.001 PHE B 433 TYR 0.014 0.001 TYR A 457 ARG 0.003 0.000 ARG B 583 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 275 LYS cc_start: 0.8884 (mttt) cc_final: 0.8651 (mttm) REVERT: A 301 TYR cc_start: 0.6651 (t80) cc_final: 0.6188 (t80) REVERT: A 326 GLN cc_start: 0.8679 (tp40) cc_final: 0.8405 (tp-100) REVERT: A 563 LEU cc_start: 0.8246 (tp) cc_final: 0.7742 (tp) REVERT: A 567 MET cc_start: 0.8595 (mtp) cc_final: 0.7980 (mtp) REVERT: A 606 MET cc_start: 0.8715 (mmm) cc_final: 0.8442 (mmm) REVERT: A 619 TYR cc_start: 0.7232 (t80) cc_final: 0.6889 (t80) REVERT: B 93 MET cc_start: 0.6159 (mtp) cc_final: 0.5937 (mtp) REVERT: B 552 LYS cc_start: 0.8789 (mttt) cc_final: 0.8512 (ttpp) REVERT: E 46 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8215 (tm-30) REVERT: K 210 ARG cc_start: 0.5837 (ttp-170) cc_final: 0.5497 (ttp80) outliers start: 14 outliers final: 13 residues processed: 197 average time/residue: 0.5082 time to fit residues: 150.8796 Evaluate side-chains 197 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain K residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.114830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.087305 restraints weight = 96561.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.090852 restraints weight = 44646.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093100 restraints weight = 27138.261| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13344 Z= 0.196 Angle : 0.521 13.188 17970 Z= 0.276 Chirality : 0.039 0.165 1979 Planarity : 0.004 0.035 2301 Dihedral : 6.576 72.046 1815 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.97 % Allowed : 14.16 % Favored : 84.88 % 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 (0.21), residues: 1593 helix: 0.65 (0.21), residues: 677 sheet: -0.51 (0.33), residues: 216 loop : -0.45 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 157 HIS 0.005 0.001 HIS A 315 PHE 0.013 0.001 PHE B 433 TYR 0.013 0.001 TYR A 457 ARG 0.003 0.000 ARG B 583 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5605.57 seconds wall clock time: 99 minutes 52.11 seconds (5992.11 seconds total)