Starting phenix.real_space_refine on Wed Apr 30 08:15:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ca1_16515/04_2025/8ca1_16515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ca1_16515/04_2025/8ca1_16515.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/cci-nas-00/data/ceres_data/8ca1_16515/04_2025/8ca1_16515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ca1_16515/04_2025/8ca1_16515.map" model { file = "/net/cci-nas-00/data/ceres_data/8ca1_16515/04_2025/8ca1_16515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ca1_16515/04_2025/8ca1_16515.cif" } 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= 0.001 sd= 0.254 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 50 5.16 5 C 5708 2.51 5 N 1566 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4465 Classifications: {'peptide': 589} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 570} Chain: "A" Number of atoms: 4465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4465 Classifications: {'peptide': 589} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 570} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.90, per 1000 atoms: 0.76 Number of scatterers: 9036 At special positions: 0 Unit cell: (85.176, 112.216, 86.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 4 15.00 O 1708 8.00 N 1566 7.00 C 5708 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 - 3.00 Amino acid : True - 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: 2.41 Conformation dependent library (CDL) restraints added in 1.0 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 6 sheets defined 67.1% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.965A pdb=" N GLN B 87 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 117 removed outlier: 4.036A pdb=" N GLY B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.878A pdb=" N GLY B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 4.130A pdb=" N LEU B 145 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 157 through 170 Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.934A pdb=" N ILE B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 193 removed outlier: 3.743A pdb=" N LEU B 191 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 208 Proline residue: B 204 - end of helix removed outlier: 3.766A pdb=" N SER B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 329 through 367 removed outlier: 4.677A pdb=" N PHE B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY B 344 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 408 removed outlier: 3.754A pdb=" N MET B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 444 removed outlier: 3.681A pdb=" N TRP B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N MET B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 Processing helix chain 'B' and resid 458 through 461 Processing helix chain 'B' and resid 465 through 493 removed outlier: 4.856A pdb=" N ASP B 480 " --> pdb=" O GLN B 476 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS B 481 " --> pdb=" O GLY B 477 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 482 " --> pdb=" O CYS B 478 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 513 Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 530 through 556 removed outlier: 3.598A pdb=" N ALA B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.771A pdb=" N VAL B 560 " --> pdb=" O LYS B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 593 removed outlier: 3.505A pdb=" N ARG B 568 " --> pdb=" O PHE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 624 removed outlier: 3.690A pdb=" N SER B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 646 Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.972A pdb=" N GLN A 87 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 117 removed outlier: 4.027A pdb=" N GLY A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.880A pdb=" N GLY A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 removed outlier: 4.126A pdb=" N LEU A 145 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.933A pdb=" N ILE A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.743A pdb=" N LEU A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 208 Proline residue: A 204 - end of helix removed outlier: 3.766A pdb=" N SER A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 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 329 through 367 removed outlier: 4.677A pdb=" N PHE A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLY A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 408 removed outlier: 3.739A pdb=" N MET A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 444 removed outlier: 3.685A pdb=" N TRP A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'A' and resid 458 through 461 Processing helix chain 'A' and resid 465 through 493 removed outlier: 4.881A pdb=" N ASP A 480 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS A 481 " --> pdb=" O GLY A 477 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 482 " --> pdb=" O CYS A 478 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 513 Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 530 through 556 removed outlier: 3.507A pdb=" N LEU A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.776A pdb=" N VAL A 560 " --> pdb=" O LYS A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 593 removed outlier: 3.506A pdb=" N ARG A 568 " --> pdb=" O PHE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 624 removed outlier: 3.687A pdb=" N SER A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 646 Processing sheet with id=AA1, first strand: chain 'B' and resid 213 through 216 removed outlier: 5.718A pdb=" N ALA B 214 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE B 263 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N CYS B 216 " --> pdb=" O PHE B 263 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N LYS B 265 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA B 282 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 235 removed outlier: 6.208A pdb=" N TYR B 241 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR B 243 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS B 317 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN B 245 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY B 315 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER B 247 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE B 313 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE B 249 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 311 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 369 Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 216 removed outlier: 5.722A pdb=" N ALA A 214 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 263 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N CYS A 216 " --> pdb=" O PHE A 263 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LYS A 265 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 282 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 235 removed outlier: 6.210A pdb=" N TYR A 241 " --> pdb=" O PRO A 319 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR A 243 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS A 317 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASN A 245 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY A 315 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER A 247 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 313 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE A 249 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 311 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 368 through 369 569 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3002 1.34 - 1.46: 1931 1.46 - 1.58: 4172 1.58 - 1.70: 1 1.70 - 1.82: 86 Bond restraints: 9192 Sorted by residual: bond pdb=" O5B FAD B 701 " pdb=" PA FAD B 701 " ideal model delta sigma weight residual 1.634 1.528 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O3P FAD B 701 " pdb=" P FAD B 701 " ideal model delta sigma weight residual 1.660 1.557 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O3P FAD A 701 " pdb=" P FAD A 701 " ideal model delta sigma weight residual 1.660 1.566 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" O5B FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sigma weight residual 1.634 1.541 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" O5' FAD B 701 " pdb=" P FAD B 701 " ideal model delta sigma weight residual 1.637 1.570 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 9187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 12176 2.75 - 5.51: 210 5.51 - 8.26: 10 8.26 - 11.02: 3 11.02 - 13.77: 1 Bond angle restraints: 12400 Sorted by residual: angle pdb=" CB MET B 301 " pdb=" CG MET B 301 " pdb=" SD MET B 301 " ideal model delta sigma weight residual 112.70 126.47 -13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" N GLU B 450 " pdb=" CA GLU B 450 " pdb=" CB GLU B 450 " ideal model delta sigma weight residual 110.12 104.63 5.49 1.47e+00 4.63e-01 1.39e+01 angle pdb=" N GLU A 450 " pdb=" CA GLU A 450 " pdb=" CB GLU A 450 " ideal model delta sigma weight residual 110.12 104.94 5.18 1.47e+00 4.63e-01 1.24e+01 angle pdb=" C MET A 301 " pdb=" CA MET A 301 " pdb=" CB MET A 301 " ideal model delta sigma weight residual 110.32 103.14 7.18 2.11e+00 2.25e-01 1.16e+01 angle pdb=" CA GLU A 450 " pdb=" CB GLU A 450 " pdb=" CG GLU A 450 " ideal model delta sigma weight residual 114.10 120.60 -6.50 2.00e+00 2.50e-01 1.06e+01 ... (remaining 12395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.11: 5199 22.11 - 44.21: 310 44.21 - 66.32: 38 66.32 - 88.43: 15 88.43 - 110.53: 4 Dihedral angle restraints: 5566 sinusoidal: 2256 harmonic: 3310 Sorted by residual: dihedral pdb=" CA LYS B 493 " pdb=" C LYS B 493 " pdb=" N ASN B 494 " pdb=" CA ASN B 494 " ideal model delta harmonic sigma weight residual 180.00 152.20 27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA LYS A 493 " pdb=" C LYS A 493 " pdb=" N ASN A 494 " pdb=" CA ASN A 494 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA THR B 368 " pdb=" C THR B 368 " pdb=" N GLN B 369 " pdb=" CA GLN B 369 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 5563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1060 0.052 - 0.104: 262 0.104 - 0.156: 48 0.156 - 0.208: 14 0.208 - 0.259: 4 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA PHE B 496 " pdb=" N PHE B 496 " pdb=" C PHE B 496 " pdb=" CB PHE B 496 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PHE A 496 " pdb=" N PHE A 496 " pdb=" C PHE A 496 " pdb=" CB PHE A 496 " 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 ILE A 303 " pdb=" N ILE A 303 " pdb=" C ILE A 303 " pdb=" CB ILE A 303 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1385 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 549 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C GLU B 549 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU B 549 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA B 550 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 549 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C GLU A 549 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU A 549 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA A 550 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 548 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C VAL B 548 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL B 548 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 549 " 0.018 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 135 2.61 - 3.18: 9451 3.18 - 3.76: 14198 3.76 - 4.33: 20206 4.33 - 4.90: 31744 Nonbonded interactions: 75734 Sorted by model distance: nonbonded pdb=" OG SER B 222 " pdb=" OE1 GLN A 369 " model vdw 2.041 3.040 nonbonded pdb=" OD2 ASP A 467 " pdb=" O2B FAD A 701 " model vdw 2.061 3.040 nonbonded pdb=" OH TYR A 202 " pdb=" OD1 ASN A 322 " model vdw 2.126 3.040 nonbonded pdb=" OH TYR B 202 " pdb=" OD1 ASN B 322 " model vdw 2.133 3.040 nonbonded pdb=" NZ LYS A 420 " pdb=" OD1 ASN A 466 " model vdw 2.154 3.120 ... (remaining 75729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.090 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.580 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.006 0.110 9192 Z= 0.289 Angle : 0.892 13.771 12400 Z= 0.505 Chirality : 0.050 0.259 1388 Planarity : 0.011 0.088 1596 Dihedral : 14.977 110.531 3454 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.23), residues: 1174 helix: -1.38 (0.17), residues: 668 sheet: -1.29 (0.54), residues: 72 loop : -0.76 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.005 TRP A 250 HIS 0.014 0.003 HIS A 182 PHE 0.046 0.004 PHE A 496 TYR 0.016 0.005 TYR A 577 ARG 0.024 0.004 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.16595 ( 569) hydrogen bonds : angle 7.48130 ( 1647) covalent geometry : bond 0.00582 ( 9192) covalent geometry : angle 0.89246 (12400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.9019 (mm) cc_final: 0.8812 (mt) REVERT: A 382 GLU cc_start: 0.8364 (pp20) cc_final: 0.8022 (pp20) REVERT: A 410 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7324 (tptt) REVERT: A 438 MET cc_start: 0.8767 (mmm) cc_final: 0.8060 (mmm) REVERT: A 479 MET cc_start: 0.8531 (mmp) cc_final: 0.8112 (mmt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1959 time to fit residues: 27.1314 Evaluate side-chains 68 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN B 183 GLN B 369 GLN B 599 HIS A 87 GLN A 183 GLN A 599 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065420 restraints weight = 31886.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.067370 restraints weight = 16467.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.068712 restraints weight = 10136.250| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9192 Z= 0.181 Angle : 0.668 8.271 12400 Z= 0.351 Chirality : 0.044 0.159 1388 Planarity : 0.004 0.036 1596 Dihedral : 9.094 77.624 1346 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.36 % Favored : 98.47 % Rotamer: Outliers : 1.17 % Allowed : 7.01 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.51 (0.24), residues: 1174 helix: 0.91 (0.19), residues: 688 sheet: -0.12 (0.59), residues: 56 loop : -0.40 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 250 HIS 0.006 0.002 HIS A 182 PHE 0.012 0.002 PHE A 422 TYR 0.014 0.001 TYR A 202 ARG 0.006 0.001 ARG A 568 Details of bonding type rmsd hydrogen bonds : bond 0.05575 ( 569) hydrogen bonds : angle 4.84668 ( 1647) covalent geometry : bond 0.00392 ( 9192) covalent geometry : angle 0.66816 (12400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.968 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: B 138 LYS cc_start: 0.8457 (mptt) cc_final: 0.8252 (mptt) REVERT: B 382 GLU cc_start: 0.8726 (pt0) cc_final: 0.8193 (pp20) REVERT: B 438 MET cc_start: 0.8963 (mmm) cc_final: 0.8294 (mmm) REVERT: B 503 MET cc_start: 0.5398 (mmt) cc_final: 0.2882 (tmm) REVERT: A 382 GLU cc_start: 0.8670 (pp20) cc_final: 0.8456 (pp20) REVERT: A 438 MET cc_start: 0.9080 (mmm) cc_final: 0.8210 (mmm) REVERT: A 479 MET cc_start: 0.8482 (mmp) cc_final: 0.8083 (mmt) outliers start: 11 outliers final: 7 residues processed: 95 average time/residue: 0.1894 time to fit residues: 26.5938 Evaluate side-chains 77 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 369 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067270 restraints weight = 32038.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.069404 restraints weight = 16471.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.070796 restraints weight = 9906.238| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9192 Z= 0.123 Angle : 0.574 13.853 12400 Z= 0.294 Chirality : 0.039 0.146 1388 Planarity : 0.004 0.034 1596 Dihedral : 8.616 60.418 1346 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.96 % Favored : 97.87 % Rotamer: Outliers : 1.38 % Allowed : 9.66 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1174 helix: 1.61 (0.19), residues: 690 sheet: 0.35 (0.59), residues: 56 loop : 0.06 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 250 HIS 0.006 0.001 HIS A 182 PHE 0.011 0.001 PHE A 422 TYR 0.009 0.001 TYR B 202 ARG 0.003 0.000 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 569) hydrogen bonds : angle 4.20027 ( 1647) covalent geometry : bond 0.00257 ( 9192) covalent geometry : angle 0.57425 (12400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LYS cc_start: 0.8424 (mptt) cc_final: 0.8187 (mptt) REVERT: B 382 GLU cc_start: 0.8663 (pt0) cc_final: 0.8108 (pp20) REVERT: B 438 MET cc_start: 0.8909 (mmm) cc_final: 0.8503 (mmm) REVERT: B 503 MET cc_start: 0.5609 (mmt) cc_final: 0.3889 (tmm) REVERT: A 382 GLU cc_start: 0.8677 (pp20) cc_final: 0.8372 (pp20) REVERT: A 438 MET cc_start: 0.9038 (mmm) cc_final: 0.8185 (mmm) REVERT: A 479 MET cc_start: 0.8476 (mmp) cc_final: 0.8047 (mmt) outliers start: 13 outliers final: 7 residues processed: 102 average time/residue: 0.1832 time to fit residues: 27.7214 Evaluate side-chains 84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 375 HIS B 618 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS A 369 GLN A 375 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.064039 restraints weight = 32422.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066017 restraints weight = 16710.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.067406 restraints weight = 10284.455| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9192 Z= 0.212 Angle : 0.649 13.126 12400 Z= 0.333 Chirality : 0.042 0.204 1388 Planarity : 0.004 0.033 1596 Dihedral : 8.393 55.347 1346 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.53 % Rotamer: Outliers : 2.44 % Allowed : 10.62 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.25), residues: 1174 helix: 1.66 (0.20), residues: 678 sheet: 0.36 (0.56), residues: 60 loop : -0.10 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 250 HIS 0.011 0.002 HIS A 182 PHE 0.013 0.002 PHE A 422 TYR 0.011 0.002 TYR A 161 ARG 0.003 0.001 ARG B 614 Details of bonding type rmsd hydrogen bonds : bond 0.05101 ( 569) hydrogen bonds : angle 4.36190 ( 1647) covalent geometry : bond 0.00472 ( 9192) covalent geometry : angle 0.64872 (12400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LYS cc_start: 0.8447 (mptt) cc_final: 0.8189 (mptt) REVERT: B 382 GLU cc_start: 0.8783 (pt0) cc_final: 0.7989 (pp20) REVERT: B 503 MET cc_start: 0.5676 (mmt) cc_final: 0.3805 (tmm) REVERT: A 382 GLU cc_start: 0.8688 (pp20) cc_final: 0.8480 (pp20) REVERT: A 438 MET cc_start: 0.9017 (mmm) cc_final: 0.8387 (mmm) REVERT: A 479 MET cc_start: 0.8382 (mmp) cc_final: 0.8032 (mmt) outliers start: 23 outliers final: 12 residues processed: 98 average time/residue: 0.1828 time to fit residues: 26.7059 Evaluate side-chains 86 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 101 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN A 87 GLN A 363 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.067917 restraints weight = 31800.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070055 restraints weight = 16162.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.071503 restraints weight = 9719.638| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9192 Z= 0.108 Angle : 0.544 12.376 12400 Z= 0.274 Chirality : 0.039 0.227 1388 Planarity : 0.003 0.031 1596 Dihedral : 7.894 60.125 1346 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.34 % Allowed : 11.46 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.26), residues: 1174 helix: 1.94 (0.20), residues: 692 sheet: -0.39 (0.56), residues: 76 loop : 0.33 (0.35), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 607 HIS 0.006 0.001 HIS B 182 PHE 0.009 0.001 PHE A 422 TYR 0.008 0.001 TYR A 202 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 569) hydrogen bonds : angle 3.89673 ( 1647) covalent geometry : bond 0.00224 ( 9192) covalent geometry : angle 0.54399 (12400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LYS cc_start: 0.8412 (mptt) cc_final: 0.8190 (mptt) REVERT: B 382 GLU cc_start: 0.8747 (pt0) cc_final: 0.7926 (pp20) REVERT: B 438 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8589 (ttp) REVERT: B 467 ASP cc_start: 0.8463 (m-30) cc_final: 0.7972 (p0) REVERT: B 503 MET cc_start: 0.5464 (mmt) cc_final: 0.4584 (tmm) REVERT: B 583 LEU cc_start: 0.8965 (mt) cc_final: 0.8614 (tt) REVERT: A 382 GLU cc_start: 0.8745 (pp20) cc_final: 0.8461 (pp20) REVERT: A 438 MET cc_start: 0.8952 (mmm) cc_final: 0.8370 (mmm) REVERT: A 467 ASP cc_start: 0.8402 (m-30) cc_final: 0.8144 (p0) REVERT: A 479 MET cc_start: 0.8366 (mmp) cc_final: 0.7983 (mmt) outliers start: 22 outliers final: 9 residues processed: 102 average time/residue: 0.1730 time to fit residues: 26.7954 Evaluate side-chains 90 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 69 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN B 498 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068280 restraints weight = 31904.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.070251 restraints weight = 16596.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071721 restraints weight = 10209.544| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9192 Z= 0.108 Angle : 0.529 11.357 12400 Z= 0.266 Chirality : 0.039 0.204 1388 Planarity : 0.003 0.034 1596 Dihedral : 7.599 65.449 1346 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.23 % Allowed : 13.16 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.26), residues: 1174 helix: 2.11 (0.20), residues: 694 sheet: -0.40 (0.59), residues: 74 loop : 0.46 (0.35), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 607 HIS 0.006 0.001 HIS B 182 PHE 0.009 0.001 PHE B 422 TYR 0.006 0.001 TYR B 202 ARG 0.002 0.000 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 569) hydrogen bonds : angle 3.86135 ( 1647) covalent geometry : bond 0.00229 ( 9192) covalent geometry : angle 0.52866 (12400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.069 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: B 138 LYS cc_start: 0.8400 (mptt) cc_final: 0.8169 (mptt) REVERT: B 380 ILE cc_start: 0.9446 (mp) cc_final: 0.9035 (mt) REVERT: B 382 GLU cc_start: 0.8733 (pt0) cc_final: 0.8006 (pp20) REVERT: B 503 MET cc_start: 0.5306 (mmt) cc_final: 0.4289 (tmm) REVERT: A 301 MET cc_start: 0.8280 (mmm) cc_final: 0.7892 (mmm) REVERT: A 353 MET cc_start: 0.8878 (mmm) cc_final: 0.8661 (mmm) REVERT: A 382 GLU cc_start: 0.8840 (pp20) cc_final: 0.8533 (pp20) REVERT: A 438 MET cc_start: 0.8991 (mmm) cc_final: 0.8394 (mmm) outliers start: 21 outliers final: 11 residues processed: 108 average time/residue: 0.1864 time to fit residues: 29.7902 Evaluate side-chains 94 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 369 GLN Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 74 optimal weight: 0.0370 chunk 80 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS B 369 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065859 restraints weight = 32498.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067846 restraints weight = 16960.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.069190 restraints weight = 10451.050| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9192 Z= 0.169 Angle : 0.598 10.568 12400 Z= 0.303 Chirality : 0.041 0.181 1388 Planarity : 0.004 0.033 1596 Dihedral : 7.613 70.202 1346 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.34 % Allowed : 13.27 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.26), residues: 1174 helix: 2.15 (0.20), residues: 680 sheet: -0.44 (0.59), residues: 74 loop : 0.41 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 607 HIS 0.009 0.002 HIS B 182 PHE 0.014 0.001 PHE B 422 TYR 0.013 0.001 TYR B 392 ARG 0.002 0.000 ARG A 386 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 569) hydrogen bonds : angle 4.02967 ( 1647) covalent geometry : bond 0.00372 ( 9192) covalent geometry : angle 0.59811 (12400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 1.116 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: B 138 LYS cc_start: 0.8401 (mptt) cc_final: 0.8181 (mptt) REVERT: B 353 MET cc_start: 0.8890 (mmm) cc_final: 0.8675 (mmm) REVERT: B 380 ILE cc_start: 0.9526 (mp) cc_final: 0.9267 (mt) REVERT: B 382 GLU cc_start: 0.8782 (pt0) cc_final: 0.8102 (pp20) REVERT: B 503 MET cc_start: 0.5256 (mmt) cc_final: 0.4049 (tmm) REVERT: A 301 MET cc_start: 0.8357 (mmm) cc_final: 0.8001 (mmm) REVERT: A 382 GLU cc_start: 0.8797 (pp20) cc_final: 0.8503 (pp20) REVERT: A 425 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7946 (mm-30) REVERT: A 438 MET cc_start: 0.9059 (mmm) cc_final: 0.8433 (mmm) outliers start: 22 outliers final: 19 residues processed: 98 average time/residue: 0.1934 time to fit residues: 27.9718 Evaluate side-chains 98 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 648 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068461 restraints weight = 32525.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070489 restraints weight = 16757.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071929 restraints weight = 10242.183| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9192 Z= 0.107 Angle : 0.538 10.434 12400 Z= 0.271 Chirality : 0.039 0.160 1388 Planarity : 0.003 0.035 1596 Dihedral : 7.478 71.369 1346 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.02 % Allowed : 13.69 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.26), residues: 1174 helix: 2.19 (0.20), residues: 694 sheet: -0.16 (0.61), residues: 72 loop : 0.44 (0.35), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 607 HIS 0.006 0.001 HIS B 182 PHE 0.012 0.001 PHE A 422 TYR 0.007 0.001 TYR B 392 ARG 0.002 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 569) hydrogen bonds : angle 3.83117 ( 1647) covalent geometry : bond 0.00228 ( 9192) covalent geometry : angle 0.53790 (12400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.089 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: B 138 LYS cc_start: 0.8396 (mptt) cc_final: 0.8152 (mptt) REVERT: B 353 MET cc_start: 0.8848 (mmm) cc_final: 0.8618 (mmm) REVERT: B 382 GLU cc_start: 0.8708 (pt0) cc_final: 0.7978 (pp20) REVERT: B 441 MET cc_start: 0.8650 (ttm) cc_final: 0.8409 (ttm) REVERT: B 503 MET cc_start: 0.5500 (mmt) cc_final: 0.4750 (tmm) REVERT: A 301 MET cc_start: 0.8349 (mmm) cc_final: 0.8099 (mmm) REVERT: A 382 GLU cc_start: 0.8817 (pp20) cc_final: 0.8515 (pp20) REVERT: A 425 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 438 MET cc_start: 0.8958 (mmm) cc_final: 0.8325 (mmm) outliers start: 19 outliers final: 15 residues processed: 104 average time/residue: 0.1953 time to fit residues: 30.0122 Evaluate side-chains 100 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 648 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.067114 restraints weight = 32213.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069104 restraints weight = 16690.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.070499 restraints weight = 10225.972| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9192 Z= 0.138 Angle : 0.566 9.797 12400 Z= 0.286 Chirality : 0.040 0.147 1388 Planarity : 0.003 0.037 1596 Dihedral : 7.518 71.716 1346 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.23 % Allowed : 13.59 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.26), residues: 1174 helix: 2.26 (0.19), residues: 706 sheet: -0.10 (0.62), residues: 72 loop : 0.43 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 607 HIS 0.008 0.002 HIS B 182 PHE 0.012 0.001 PHE A 422 TYR 0.008 0.001 TYR B 392 ARG 0.002 0.000 ARG B 532 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 569) hydrogen bonds : angle 3.84761 ( 1647) covalent geometry : bond 0.00306 ( 9192) covalent geometry : angle 0.56571 (12400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.979 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: B 138 LYS cc_start: 0.8426 (mptt) cc_final: 0.8218 (mptt) REVERT: B 382 GLU cc_start: 0.8730 (pt0) cc_final: 0.8005 (pp20) REVERT: B 441 MET cc_start: 0.8592 (ttm) cc_final: 0.8348 (ttm) REVERT: B 503 MET cc_start: 0.5132 (mmt) cc_final: 0.4130 (tmm) REVERT: A 301 MET cc_start: 0.8361 (mmm) cc_final: 0.8124 (mmm) REVERT: A 382 GLU cc_start: 0.8765 (pp20) cc_final: 0.8505 (pp20) REVERT: A 425 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8033 (mm-30) REVERT: A 438 MET cc_start: 0.8969 (mmm) cc_final: 0.8338 (mmm) outliers start: 21 outliers final: 19 residues processed: 100 average time/residue: 0.1976 time to fit residues: 29.1978 Evaluate side-chains 101 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 648 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 101 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.067238 restraints weight = 32163.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069248 restraints weight = 16749.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070711 restraints weight = 10307.173| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9192 Z= 0.131 Angle : 0.564 9.629 12400 Z= 0.286 Chirality : 0.040 0.284 1388 Planarity : 0.003 0.037 1596 Dihedral : 7.454 72.565 1346 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.91 % Allowed : 14.12 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.26), residues: 1174 helix: 2.23 (0.19), residues: 706 sheet: -0.07 (0.62), residues: 72 loop : 0.42 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 607 HIS 0.007 0.001 HIS B 182 PHE 0.013 0.001 PHE B 422 TYR 0.010 0.001 TYR B 392 ARG 0.003 0.000 ARG A 451 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 569) hydrogen bonds : angle 3.83982 ( 1647) covalent geometry : bond 0.00290 ( 9192) covalent geometry : angle 0.56359 (12400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 MET cc_start: 0.8714 (ppp) cc_final: 0.8096 (ppp) REVERT: B 382 GLU cc_start: 0.8734 (pt0) cc_final: 0.8018 (pp20) REVERT: B 441 MET cc_start: 0.8665 (ttm) cc_final: 0.8410 (ttm) REVERT: B 503 MET cc_start: 0.5120 (mmt) cc_final: 0.4165 (tmm) REVERT: A 382 GLU cc_start: 0.8766 (pp20) cc_final: 0.8513 (pp20) REVERT: A 438 MET cc_start: 0.8972 (mmm) cc_final: 0.8332 (mmm) REVERT: A 455 ASP cc_start: 0.8727 (m-30) cc_final: 0.7850 (m-30) outliers start: 18 outliers final: 16 residues processed: 96 average time/residue: 0.1912 time to fit residues: 27.1430 Evaluate side-chains 96 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 648 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 58 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 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 = 0.3289 r_free = 0.3289 target = 0.076851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.067594 restraints weight = 31949.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.069613 restraints weight = 16580.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.071006 restraints weight = 10150.881| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9192 Z= 0.126 Angle : 0.569 9.479 12400 Z= 0.288 Chirality : 0.040 0.263 1388 Planarity : 0.003 0.038 1596 Dihedral : 7.427 72.625 1346 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.02 % Allowed : 14.01 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.26), residues: 1174 helix: 2.23 (0.19), residues: 706 sheet: -0.10 (0.62), residues: 72 loop : 0.45 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 607 HIS 0.007 0.001 HIS B 182 PHE 0.012 0.001 PHE B 422 TYR 0.009 0.001 TYR B 392 ARG 0.002 0.000 ARG A 451 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 569) hydrogen bonds : angle 3.81935 ( 1647) covalent geometry : bond 0.00277 ( 9192) covalent geometry : angle 0.56905 (12400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.94 seconds wall clock time: 45 minutes 59.26 seconds (2759.26 seconds total)