Starting phenix.real_space_refine on Thu Feb 13 20:12:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ca1_16515/02_2025/8ca1_16515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ca1_16515/02_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_16515/02_2025/8ca1_16515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ca1_16515/02_2025/8ca1_16515.map" model { file = "/net/cci-nas-00/data/ceres_data/8ca1_16515/02_2025/8ca1_16515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ca1_16515/02_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-5592/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: 7.00, per 1000 atoms: 0.77 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: 2.65 Conformation dependent library (CDL) restraints added in 1.1 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: 0.93 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: 2.79 Time building geometry restraints manager: 2.97 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: 7.110 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.010 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- 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= 0.396 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 *********************** 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 : 1.104 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: 0.2104 time to fit residues: 28.9647 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 : 0.985 ------------------------------------------------------------------------------- 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 = 31886.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.067372 restraints weight = 16468.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.068754 restraints weight = 10132.527| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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= 0.257 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 *********************** 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 : 1.061 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: 0.8458 (mptt) cc_final: 0.8254 (mptt) REVERT: B 382 GLU cc_start: 0.8721 (pt0) cc_final: 0.8189 (pp20) REVERT: B 438 MET cc_start: 0.8963 (mmm) cc_final: 0.8295 (mmm) REVERT: B 503 MET cc_start: 0.5393 (mmt) cc_final: 0.2878 (tmm) REVERT: A 382 GLU cc_start: 0.8666 (pp20) cc_final: 0.8453 (pp20) REVERT: A 438 MET cc_start: 0.9078 (mmm) cc_final: 0.8209 (mmm) REVERT: A 479 MET cc_start: 0.8484 (mmp) cc_final: 0.8084 (mmt) outliers start: 11 outliers final: 7 residues processed: 95 average time/residue: 0.1960 time to fit residues: 27.4597 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 : 1.029 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.076483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.067276 restraints weight = 32046.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069397 restraints weight = 16394.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070658 restraints weight = 9953.701| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2856 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= 0.167 Angle : 0.575 13.693 12400 Z= 0.294 Chirality : 0.039 0.146 1388 Planarity : 0.004 0.034 1596 Dihedral : 8.615 60.674 1346 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.96 % Favored : 97.87 % Rotamer: Outliers : 1.27 % Allowed : 9.77 % 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: 1.42 (0.25), residues: 1174 helix: 1.60 (0.19), residues: 690 sheet: 0.34 (0.58), residues: 56 loop : 0.04 (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 0.010 0.001 TYR B 202 ARG 0.003 0.000 ARG B 205 *********************** 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 108 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 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: B 87 GLN cc_start: 0.7156 (mt0) cc_final: 0.6937 (mt0) REVERT: B 138 LYS cc_start: 0.8423 (mptt) cc_final: 0.8188 (mptt) REVERT: B 382 GLU cc_start: 0.8724 (pt0) cc_final: 0.8112 (pp20) REVERT: B 438 MET cc_start: 0.8911 (mmm) cc_final: 0.8502 (mmm) REVERT: B 503 MET cc_start: 0.5612 (mmt) cc_final: 0.3951 (tmm) REVERT: A 382 GLU cc_start: 0.8680 (pp20) cc_final: 0.8376 (pp20) REVERT: A 438 MET cc_start: 0.9035 (mmm) cc_final: 0.8198 (mmm) REVERT: A 441 MET cc_start: 0.8723 (ttm) cc_final: 0.8514 (ttm) REVERT: A 479 MET cc_start: 0.8478 (mmp) cc_final: 0.8048 (mmt) outliers start: 12 outliers final: 7 residues processed: 101 average time/residue: 0.1890 time to fit residues: 28.5107 Evaluate side-chains 85 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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: 0.8980 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN B 375 HIS B 618 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064416 restraints weight = 32421.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066379 restraints weight = 16785.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067748 restraints weight = 10347.331| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9192 Z= 0.297 Angle : 0.641 13.098 12400 Z= 0.329 Chirality : 0.042 0.208 1388 Planarity : 0.004 0.033 1596 Dihedral : 8.384 55.300 1346 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.34 % Allowed : 10.51 % Favored : 87.15 % 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: 1.69 (0.20), residues: 678 sheet: -0.40 (0.55), residues: 74 loop : 0.11 (0.33), residues: 422 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 B 422 TYR 0.010 0.002 TYR A 161 ARG 0.004 0.001 ARG A 342 *********************** 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: 22 poor density : 89 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LYS cc_start: 0.8446 (mptt) cc_final: 0.8208 (mptt) REVERT: B 382 GLU cc_start: 0.8767 (pt0) cc_final: 0.8141 (pp20) REVERT: B 503 MET cc_start: 0.5688 (mmt) cc_final: 0.3780 (tmm) REVERT: B 583 LEU cc_start: 0.8976 (mt) cc_final: 0.8661 (tt) REVERT: A 382 GLU cc_start: 0.8672 (pp20) cc_final: 0.8471 (pp20) REVERT: A 438 MET cc_start: 0.9015 (mmm) cc_final: 0.8372 (mmm) REVERT: A 479 MET cc_start: 0.8348 (mmp) cc_final: 0.8016 (mmt) outliers start: 22 outliers final: 12 residues processed: 98 average time/residue: 0.1904 time to fit residues: 27.7896 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 : 0.999 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 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 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN A 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.075275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066026 restraints weight = 32178.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.068000 restraints weight = 16551.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.069424 restraints weight = 10149.653| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3377 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= 0.196 Angle : 0.571 12.158 12400 Z= 0.289 Chirality : 0.040 0.232 1388 Planarity : 0.003 0.031 1596 Dihedral : 8.098 55.564 1346 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.23 % Allowed : 11.57 % 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: 1.68 (0.25), residues: 1174 helix: 1.92 (0.20), residues: 678 sheet: 0.43 (0.59), residues: 60 loop : 0.01 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 607 HIS 0.008 0.001 HIS B 182 PHE 0.011 0.001 PHE A 422 TYR 0.008 0.001 TYR B 202 ARG 0.003 0.000 ARG A 614 *********************** 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 104 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LYS cc_start: 0.8435 (mptt) cc_final: 0.8191 (mptt) REVERT: B 382 GLU cc_start: 0.8756 (pt0) cc_final: 0.8100 (pp20) REVERT: B 503 MET cc_start: 0.5382 (mmt) cc_final: 0.4163 (tmm) REVERT: A 382 GLU cc_start: 0.8707 (pp20) cc_final: 0.8469 (pp20) REVERT: A 438 MET cc_start: 0.8997 (mmm) cc_final: 0.8290 (mmm) REVERT: A 479 MET cc_start: 0.8385 (mmp) cc_final: 0.8006 (mmt) outliers start: 21 outliers final: 11 residues processed: 96 average time/residue: 0.1955 time to fit residues: 28.3979 Evaluate side-chains 87 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 244 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 488 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 MET 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: 3.9990 chunk 81 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 107 optimal weight: 0.0040 chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN B 498 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.066738 restraints weight = 31858.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.068756 restraints weight = 16533.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.070242 restraints weight = 10183.339| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9192 Z= 0.179 Angle : 0.557 11.338 12400 Z= 0.280 Chirality : 0.040 0.198 1388 Planarity : 0.003 0.035 1596 Dihedral : 7.797 62.333 1346 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.02 % Allowed : 13.06 % Favored : 84.93 % 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: 1.79 (0.26), residues: 1174 helix: 1.93 (0.20), residues: 694 sheet: -0.52 (0.59), residues: 74 loop : 0.33 (0.35), residues: 406 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 409 TYR 0.007 0.001 TYR B 202 ARG 0.002 0.000 ARG A 532 *********************** 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 104 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.162 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: 0.8413 (mptt) cc_final: 0.8201 (mptt) REVERT: B 380 ILE cc_start: 0.9474 (mp) cc_final: 0.9034 (mt) REVERT: B 382 GLU cc_start: 0.8757 (pt0) cc_final: 0.8093 (pp20) REVERT: B 400 MET cc_start: 0.8953 (ttt) cc_final: 0.8640 (ttt) REVERT: B 503 MET cc_start: 0.5188 (mmt) cc_final: 0.4044 (tmm) REVERT: A 382 GLU cc_start: 0.8813 (pp20) cc_final: 0.8516 (pp20) REVERT: A 438 MET cc_start: 0.9003 (mmm) cc_final: 0.8413 (mmm) REVERT: A 441 MET cc_start: 0.8657 (ttm) cc_final: 0.8422 (ttm) REVERT: A 479 MET cc_start: 0.8351 (mmp) cc_final: 0.7975 (mmt) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 0.1956 time to fit residues: 28.1277 Evaluate side-chains 87 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 450 GLU 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 401 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: 0.6980 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.064999 restraints weight = 32498.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.066946 restraints weight = 16914.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.068380 restraints weight = 10477.642| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9192 Z= 0.275 Angle : 0.620 10.703 12400 Z= 0.312 Chirality : 0.041 0.174 1388 Planarity : 0.004 0.030 1596 Dihedral : 7.790 67.670 1346 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.02 % Allowed : 13.27 % Favored : 84.71 % 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: 1.73 (0.25), residues: 1174 helix: 1.98 (0.20), residues: 680 sheet: -0.61 (0.59), residues: 74 loop : 0.20 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 250 HIS 0.010 0.002 HIS A 182 PHE 0.014 0.002 PHE A 422 TYR 0.008 0.001 TYR A 399 ARG 0.002 0.000 ARG A 386 *********************** 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 97 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 1.034 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: 0.8430 (mptt) cc_final: 0.8210 (mptt) REVERT: B 382 GLU cc_start: 0.8796 (pt0) cc_final: 0.8095 (pp20) REVERT: B 400 MET cc_start: 0.9033 (ttt) cc_final: 0.8669 (ttt) REVERT: B 503 MET cc_start: 0.5460 (mmt) cc_final: 0.4092 (tmm) REVERT: A 382 GLU cc_start: 0.8754 (pp20) cc_final: 0.8515 (pp20) REVERT: A 438 MET cc_start: 0.8995 (mmm) cc_final: 0.8321 (mmm) REVERT: A 441 MET cc_start: 0.8680 (ttm) cc_final: 0.8450 (ttm) REVERT: A 467 ASP cc_start: 0.8411 (m-30) cc_final: 0.8190 (m-30) REVERT: A 479 MET cc_start: 0.8382 (mmp) cc_final: 0.7993 (mmt) outliers start: 19 outliers final: 15 residues processed: 90 average time/residue: 0.1854 time to fit residues: 24.9078 Evaluate side-chains 91 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 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 B residue 559 ILE 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 488 LEU Chi-restraints excluded: chain A residue 559 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** A 369 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.077318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.067966 restraints weight = 32414.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069987 restraints weight = 16717.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.071417 restraints weight = 10290.442| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9192 Z= 0.145 Angle : 0.552 10.725 12400 Z= 0.272 Chirality : 0.039 0.163 1388 Planarity : 0.003 0.031 1596 Dihedral : 7.551 68.576 1346 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.49 % Allowed : 13.59 % Favored : 84.93 % 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: 1.98 (0.26), residues: 1174 helix: 2.11 (0.20), residues: 694 sheet: -0.24 (0.60), residues: 72 loop : 0.31 (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 A 182 PHE 0.012 0.001 PHE B 422 TYR 0.007 0.001 TYR B 202 ARG 0.002 0.000 ARG B 457 *********************** 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 107 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.018 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: 0.8401 (mptt) cc_final: 0.8169 (mptt) REVERT: B 301 MET cc_start: 0.8349 (mmm) cc_final: 0.8131 (mmm) REVERT: B 382 GLU cc_start: 0.8763 (pt0) cc_final: 0.8003 (pp20) REVERT: B 400 MET cc_start: 0.8921 (ttt) cc_final: 0.8646 (ttt) REVERT: B 503 MET cc_start: 0.5238 (mmt) cc_final: 0.4301 (tmm) REVERT: A 301 MET cc_start: 0.8334 (mmm) cc_final: 0.8088 (mmm) REVERT: A 382 GLU cc_start: 0.8814 (pp20) cc_final: 0.8530 (pp20) REVERT: A 438 MET cc_start: 0.8956 (mmm) cc_final: 0.8352 (mmm) REVERT: A 441 MET cc_start: 0.8608 (ttm) cc_final: 0.8377 (ttm) REVERT: A 479 MET cc_start: 0.8328 (mmp) cc_final: 0.7977 (mmt) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.1841 time to fit residues: 28.2043 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 : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 401 LEU Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.066764 restraints weight = 32300.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.068755 restraints weight = 16716.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070123 restraints weight = 10315.550| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9192 Z= 0.199 Angle : 0.574 10.163 12400 Z= 0.289 Chirality : 0.040 0.137 1388 Planarity : 0.003 0.033 1596 Dihedral : 7.523 70.436 1346 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.91 % Allowed : 14.23 % Favored : 83.86 % 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: 2.10 (0.26), residues: 1174 helix: 2.26 (0.20), residues: 680 sheet: -0.15 (0.61), residues: 72 loop : 0.32 (0.34), residues: 422 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 0.015 0.001 PHE B 422 TYR 0.017 0.001 TYR B 392 ARG 0.002 0.000 ARG A 451 *********************** 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 99 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.063 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 382 GLU cc_start: 0.8777 (pt0) cc_final: 0.8021 (pp20) REVERT: B 400 MET cc_start: 0.8963 (ttt) cc_final: 0.8644 (ttt) REVERT: B 503 MET cc_start: 0.5322 (mmt) cc_final: 0.4104 (tmm) REVERT: A 382 GLU cc_start: 0.8771 (pp20) cc_final: 0.8508 (pp20) REVERT: A 438 MET cc_start: 0.8969 (mmm) cc_final: 0.8361 (mmm) REVERT: A 479 MET cc_start: 0.8355 (mmp) cc_final: 0.8009 (mmt) outliers start: 18 outliers final: 15 residues processed: 94 average time/residue: 0.1805 time to fit residues: 25.4416 Evaluate side-chains 91 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 284 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 345 MET 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 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 488 LEU Chi-restraints excluded: chain A residue 516 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 92 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.068556 restraints weight = 32049.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070535 restraints weight = 16526.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072030 restraints weight = 10210.998| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9192 Z= 0.148 Angle : 0.552 10.113 12400 Z= 0.274 Chirality : 0.039 0.139 1388 Planarity : 0.003 0.035 1596 Dihedral : 7.387 70.838 1346 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.27 % Allowed : 14.86 % Favored : 83.86 % 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: 2.22 (0.19), residues: 706 sheet: -0.05 (0.61), residues: 72 loop : 0.43 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 607 HIS 0.005 0.001 HIS B 182 PHE 0.013 0.001 PHE B 422 TYR 0.010 0.001 TYR B 392 ARG 0.002 0.000 ARG A 457 ********************** 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 100 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.073 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 382 GLU cc_start: 0.8760 (pt0) cc_final: 0.8023 (pp20) REVERT: B 400 MET cc_start: 0.8900 (ttt) cc_final: 0.8639 (ttt) REVERT: B 441 MET cc_start: 0.8631 (ttm) cc_final: 0.8386 (ttm) REVERT: B 503 MET cc_start: 0.5200 (mmt) cc_final: 0.4356 (tmm) REVERT: A 382 GLU cc_start: 0.8794 (pp20) cc_final: 0.8481 (pp20) REVERT: A 438 MET cc_start: 0.8912 (mmm) cc_final: 0.8311 (mmm) outliers start: 12 outliers final: 10 residues processed: 97 average time/residue: 0.1759 time to fit residues: 25.9164 Evaluate side-chains 93 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 450 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069481 restraints weight = 31874.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.071549 restraints weight = 16584.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072984 restraints weight = 10170.264| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9192 Z= 0.145 Angle : 0.553 9.779 12400 Z= 0.274 Chirality : 0.039 0.153 1388 Planarity : 0.003 0.037 1596 Dihedral : 7.202 70.979 1346 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.38 % Allowed : 14.97 % Favored : 83.65 % 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: 2.32 (0.26), residues: 1174 helix: 2.32 (0.19), residues: 706 sheet: 0.00 (0.61), residues: 72 loop : 0.48 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 250 HIS 0.005 0.001 HIS B 182 PHE 0.012 0.001 PHE B 422 TYR 0.008 0.001 TYR B 392 ARG 0.002 0.000 ARG B 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2220.77 seconds wall clock time: 41 minutes 21.90 seconds (2481.90 seconds total)