Starting phenix.real_space_refine on Mon May 12 09:23:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fva_50794/05_2025/9fva_50794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fva_50794/05_2025/9fva_50794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fva_50794/05_2025/9fva_50794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fva_50794/05_2025/9fva_50794.map" model { file = "/net/cci-nas-00/data/ceres_data/9fva_50794/05_2025/9fva_50794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fva_50794/05_2025/9fva_50794.cif" } resolution = 4.4 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= 0.009 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5590 2.51 5 N 1536 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8822 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Chain: "A" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Time building chain proxies: 5.79, per 1000 atoms: 0.66 Number of scatterers: 8822 At special positions: 0 Unit cell: (120.36, 68.68, 135.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1642 8.00 N 1536 7.00 C 5590 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: 2.15 Conformation dependent library (CDL) restraints added in 1.0 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 62.5% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 15 through 20 removed outlier: 4.502A pdb=" N THR B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 15 through 20' Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 53 removed outlier: 4.127A pdb=" N ILE B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 66 through 109 Processing helix chain 'B' and resid 123 through 164 removed outlier: 3.650A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 213 Proline residue: B 176 - end of helix removed outlier: 4.016A pdb=" N MET B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 removed outlier: 3.673A pdb=" N VAL B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 270 removed outlier: 3.710A pdb=" N SER B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 253 - end of helix removed outlier: 3.567A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 302 removed outlier: 3.557A pdb=" N VAL B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ARG B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 303 through 322 Processing helix chain 'B' and resid 381 through 387 removed outlier: 4.158A pdb=" N ALA B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 446 through 458 Processing helix chain 'B' and resid 482 through 497 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 538 through 544 Processing helix chain 'B' and resid 561 through 568 removed outlier: 3.989A pdb=" N HIS B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 580 Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.509A pdb=" N THR A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 47 removed outlier: 4.182A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 66 through 107 removed outlier: 4.212A pdb=" N LEU A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.925A pdb=" N PHE A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 129 Processing helix chain 'A' and resid 129 through 148 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 195 Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 196 through 213 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 222 through 270 removed outlier: 3.698A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.655A pdb=" N ILE A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.620A pdb=" N MET A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 303 removed outlier: 4.021A pdb=" N THR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.547A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.534A pdb=" N GLN A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.833A pdb=" N ALA A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.591A pdb=" N ILE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.646A pdb=" N ALA A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 514 through 528 removed outlier: 3.662A pdb=" N LYS A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.620A pdb=" N GLU A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 568' Processing helix chain 'A' and resid 571 through 580 Processing sheet with id=AA1, first strand: chain 'B' and resid 342 through 345 removed outlier: 4.114A pdb=" N VAL B 342 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 366 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 348 through 349 removed outlier: 3.755A pdb=" N GLU B 397 " --> pdb=" O THR B 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 502 through 504 removed outlier: 6.423A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 372 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 534 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL B 551 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL B 375 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL B 550 " --> pdb=" O VAL B 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 removed outlier: 7.106A pdb=" N ALA A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.783A pdb=" N ASP A 431 " --> pdb=" O ILE A 474 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1404 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: 2.31 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2323 1.33 - 1.45: 1499 1.45 - 1.58: 5024 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 8950 Sorted by residual: bond pdb=" C GLY A 110 " pdb=" N MET A 111 " ideal model delta sigma weight residual 1.327 1.392 -0.065 1.71e-02 3.42e+03 1.44e+01 bond pdb=" N THR B 432 " pdb=" CA THR B 432 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.27e-02 6.20e+03 9.24e+00 bond pdb=" N VAL B 433 " pdb=" CA VAL B 433 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.24e-02 6.50e+03 9.02e+00 bond pdb=" N ARG B 61 " pdb=" CA ARG B 61 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.00e-02 1.00e+04 8.96e+00 bond pdb=" N ILE A 463 " pdb=" CA ILE A 463 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.40e+00 ... (remaining 8945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 11759 2.85 - 5.71: 297 5.71 - 8.56: 29 8.56 - 11.41: 6 11.41 - 14.26: 1 Bond angle restraints: 12092 Sorted by residual: angle pdb=" N ASP B 431 " pdb=" CA ASP B 431 " pdb=" C ASP B 431 " ideal model delta sigma weight residual 109.52 99.24 10.28 1.55e+00 4.16e-01 4.40e+01 angle pdb=" CA ARG A 493 " pdb=" C ARG A 493 " pdb=" O ARG A 493 " ideal model delta sigma weight residual 121.40 115.69 5.71 1.11e+00 8.12e-01 2.65e+01 angle pdb=" N PRO A 357 " pdb=" CA PRO A 357 " pdb=" C PRO A 357 " ideal model delta sigma weight residual 111.14 103.45 7.69 1.56e+00 4.11e-01 2.43e+01 angle pdb=" CA GLU B 514 " pdb=" CB GLU B 514 " pdb=" CG GLU B 514 " ideal model delta sigma weight residual 114.10 123.67 -9.57 2.00e+00 2.50e-01 2.29e+01 angle pdb=" CB MET B 44 " pdb=" CG MET B 44 " pdb=" SD MET B 44 " ideal model delta sigma weight residual 112.70 126.96 -14.26 3.00e+00 1.11e-01 2.26e+01 ... (remaining 12087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4690 17.80 - 35.60: 590 35.60 - 53.40: 145 53.40 - 71.19: 22 71.19 - 88.99: 7 Dihedral angle restraints: 5454 sinusoidal: 2164 harmonic: 3290 Sorted by residual: dihedral pdb=" CA GLN B 418 " pdb=" C GLN B 418 " pdb=" N VAL B 419 " pdb=" CA VAL B 419 " ideal model delta harmonic sigma weight residual 180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ARG B 416 " pdb=" C ARG B 416 " pdb=" N ASN B 417 " pdb=" CA ASN B 417 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA THR B 320 " pdb=" C THR B 320 " pdb=" N ILE B 321 " pdb=" CA ILE B 321 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1126 0.055 - 0.111: 256 0.111 - 0.166: 40 0.166 - 0.221: 9 0.221 - 0.277: 9 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA ASP B 431 " pdb=" N ASP B 431 " pdb=" C ASP B 431 " pdb=" CB ASP B 431 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ARG A 493 " pdb=" N ARG A 493 " pdb=" C ARG A 493 " pdb=" CB ARG A 493 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE A 463 " pdb=" N ILE A 463 " pdb=" C ILE A 463 " pdb=" CB ILE A 463 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1437 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 492 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C ALA A 492 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA A 492 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 493 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 514 " -0.013 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C GLU B 514 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU B 514 " -0.016 2.00e-02 2.50e+03 pdb=" N SER B 515 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 127 " -0.197 9.50e-02 1.11e+02 8.88e-02 5.55e+00 pdb=" NE ARG B 127 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 127 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 127 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 127 " -0.002 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1007 2.74 - 3.28: 9856 3.28 - 3.82: 14817 3.82 - 4.36: 16989 4.36 - 4.90: 27207 Nonbonded interactions: 69876 Sorted by model distance: nonbonded pdb=" O TYR B 458 " pdb=" NH2 ARG B 488 " model vdw 2.206 3.120 nonbonded pdb=" OD2 ASP A 53 " pdb=" OG1 THR A 280 " model vdw 2.217 3.040 nonbonded pdb=" O MET A 160 " pdb=" N SER A 164 " model vdw 2.248 3.120 nonbonded pdb=" O ARG A 78 " pdb=" OG SER A 82 " model vdw 2.254 3.040 nonbonded pdb=" O LEU B 502 " pdb=" OG SER B 532 " model vdw 2.257 3.040 ... (remaining 69871 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: 0.04 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: 3.500 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: 0.080 Process input model: 22.110 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.005 0.065 8950 Z= 0.306 Angle : 1.037 14.264 12092 Z= 0.589 Chirality : 0.052 0.277 1440 Planarity : 0.006 0.089 1532 Dihedral : 16.479 88.993 3326 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 0.72 % Allowed : 24.59 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1134 helix: -0.11 (0.20), residues: 660 sheet: -1.93 (0.67), residues: 53 loop : -2.07 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 17 HIS 0.008 0.002 HIS B 576 PHE 0.038 0.002 PHE A 13 TYR 0.013 0.001 TYR B 439 ARG 0.015 0.001 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.15433 ( 478) hydrogen bonds : angle 6.43903 ( 1404) covalent geometry : bond 0.00546 ( 8950) covalent geometry : angle 1.03718 (12092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 205 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ASP cc_start: 0.7772 (t0) cc_final: 0.7567 (t0) REVERT: B 100 MET cc_start: 0.9028 (tpp) cc_final: 0.8751 (mmp) REVERT: B 132 SER cc_start: 0.9215 (t) cc_final: 0.8875 (p) REVERT: B 133 GLU cc_start: 0.7868 (mp0) cc_final: 0.7445 (mp0) REVERT: B 236 ARG cc_start: 0.8898 (mmp-170) cc_final: 0.8622 (mmp-170) REVERT: A 98 MET cc_start: 0.8296 (tmm) cc_final: 0.7639 (tmm) REVERT: A 126 SER cc_start: 0.9404 (m) cc_final: 0.9200 (p) outliers start: 7 outliers final: 2 residues processed: 207 average time/residue: 0.1933 time to fit residues: 55.7055 Evaluate side-chains 185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 HIS A 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.113595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.090580 restraints weight = 29916.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.093363 restraints weight = 20283.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.095443 restraints weight = 15082.743| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8950 Z= 0.140 Angle : 0.655 8.391 12092 Z= 0.342 Chirality : 0.044 0.222 1440 Planarity : 0.005 0.046 1532 Dihedral : 5.239 23.265 1238 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.21 % Allowed : 3.41 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1134 helix: 0.33 (0.20), residues: 665 sheet: -1.16 (0.67), residues: 59 loop : -1.98 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 91 HIS 0.005 0.001 HIS B 576 PHE 0.013 0.001 PHE A 392 TYR 0.016 0.001 TYR B 87 ARG 0.009 0.001 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 478) hydrogen bonds : angle 4.92003 ( 1404) covalent geometry : bond 0.00280 ( 8950) covalent geometry : angle 0.65478 (12092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.8935 (tmm) cc_final: 0.8735 (tmm) REVERT: B 45 LEU cc_start: 0.9465 (mt) cc_final: 0.9258 (mt) REVERT: B 47 LEU cc_start: 0.9146 (mt) cc_final: 0.8876 (mt) REVERT: B 132 SER cc_start: 0.9417 (t) cc_final: 0.9035 (p) REVERT: B 133 GLU cc_start: 0.8057 (mp0) cc_final: 0.7518 (mp0) REVERT: B 312 MET cc_start: 0.5322 (tpp) cc_final: 0.5075 (tpp) REVERT: B 430 ASN cc_start: 0.7890 (p0) cc_final: 0.7572 (p0) REVERT: B 456 MET cc_start: 0.9070 (mpp) cc_final: 0.8765 (mpp) REVERT: A 44 MET cc_start: 0.8930 (tmm) cc_final: 0.8490 (tmm) REVERT: A 45 LEU cc_start: 0.9416 (mt) cc_final: 0.9122 (mt) REVERT: A 126 SER cc_start: 0.9381 (m) cc_final: 0.9090 (p) REVERT: A 219 ILE cc_start: 0.9258 (mm) cc_final: 0.8996 (mm) REVERT: A 229 ARG cc_start: 0.8573 (tpp80) cc_final: 0.8267 (ttm170) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.2033 time to fit residues: 62.2087 Evaluate side-chains 177 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 27 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 52 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.112886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.089724 restraints weight = 30441.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092412 restraints weight = 20895.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.094403 restraints weight = 15653.137| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8950 Z= 0.129 Angle : 0.641 9.132 12092 Z= 0.329 Chirality : 0.042 0.211 1440 Planarity : 0.004 0.047 1532 Dihedral : 5.102 22.997 1238 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1134 helix: 0.49 (0.20), residues: 663 sheet: -0.51 (0.80), residues: 47 loop : -1.95 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 91 HIS 0.005 0.001 HIS B 537 PHE 0.011 0.001 PHE A 23 TYR 0.013 0.001 TYR A 572 ARG 0.004 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 478) hydrogen bonds : angle 4.73397 ( 1404) covalent geometry : bond 0.00258 ( 8950) covalent geometry : angle 0.64118 (12092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 1.008 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 44 MET cc_start: 0.8956 (tmm) cc_final: 0.8732 (tmm) REVERT: B 45 LEU cc_start: 0.9459 (mt) cc_final: 0.9204 (mt) REVERT: B 47 LEU cc_start: 0.9144 (mt) cc_final: 0.8892 (mt) REVERT: B 75 MET cc_start: 0.9248 (ttp) cc_final: 0.8985 (ttt) REVERT: B 132 SER cc_start: 0.9467 (t) cc_final: 0.9046 (p) REVERT: B 133 GLU cc_start: 0.8189 (mp0) cc_final: 0.7551 (mp0) REVERT: B 248 SER cc_start: 0.9553 (t) cc_final: 0.9341 (p) REVERT: B 388 LEU cc_start: 0.8082 (mm) cc_final: 0.7872 (mm) REVERT: B 430 ASN cc_start: 0.7999 (p0) cc_final: 0.7735 (p0) REVERT: B 456 MET cc_start: 0.9126 (mpp) cc_final: 0.8789 (mmm) REVERT: A 44 MET cc_start: 0.8951 (tmm) cc_final: 0.8506 (tmm) REVERT: A 45 LEU cc_start: 0.9424 (mt) cc_final: 0.9103 (mt) REVERT: A 126 SER cc_start: 0.9415 (m) cc_final: 0.9158 (p) REVERT: A 219 ILE cc_start: 0.9244 (mm) cc_final: 0.9038 (mm) REVERT: A 229 ARG cc_start: 0.8524 (tpp80) cc_final: 0.8167 (ttm170) REVERT: A 248 SER cc_start: 0.9546 (t) cc_final: 0.9280 (p) REVERT: A 449 GLN cc_start: 0.9375 (mt0) cc_final: 0.8939 (mp10) REVERT: A 451 GLU cc_start: 0.8860 (pt0) cc_final: 0.8297 (pp20) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.2004 time to fit residues: 60.7405 Evaluate side-chains 181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 99 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** 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 = 0.3982 r_free = 0.3982 target = 0.115157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.091744 restraints weight = 31602.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.094426 restraints weight = 22092.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.096444 restraints weight = 16784.914| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8950 Z= 0.123 Angle : 0.665 13.759 12092 Z= 0.337 Chirality : 0.043 0.263 1440 Planarity : 0.004 0.051 1532 Dihedral : 5.013 21.685 1238 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1134 helix: 0.47 (0.20), residues: 659 sheet: -0.55 (0.72), residues: 57 loop : -1.98 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 91 HIS 0.004 0.001 HIS B 576 PHE 0.014 0.001 PHE A 23 TYR 0.012 0.001 TYR A 458 ARG 0.004 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 478) hydrogen bonds : angle 4.66346 ( 1404) covalent geometry : bond 0.00251 ( 8950) covalent geometry : angle 0.66500 (12092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.029 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 45 LEU cc_start: 0.9399 (mt) cc_final: 0.9154 (mt) REVERT: B 47 LEU cc_start: 0.9054 (mt) cc_final: 0.8733 (mt) REVERT: B 132 SER cc_start: 0.9470 (t) cc_final: 0.9183 (p) REVERT: B 133 GLU cc_start: 0.8250 (mp0) cc_final: 0.7772 (mp0) REVERT: B 248 SER cc_start: 0.9522 (t) cc_final: 0.9320 (p) REVERT: B 312 MET cc_start: 0.5361 (tpp) cc_final: 0.4270 (tpp) REVERT: B 430 ASN cc_start: 0.8082 (p0) cc_final: 0.7795 (p0) REVERT: B 431 ASP cc_start: 0.7301 (t0) cc_final: 0.6916 (t0) REVERT: B 456 MET cc_start: 0.9116 (mpp) cc_final: 0.8830 (mpp) REVERT: B 474 ILE cc_start: 0.8203 (mm) cc_final: 0.7994 (mp) REVERT: A 44 MET cc_start: 0.8899 (tmm) cc_final: 0.8537 (tmm) REVERT: A 45 LEU cc_start: 0.9418 (mt) cc_final: 0.9115 (mt) REVERT: A 126 SER cc_start: 0.9450 (m) cc_final: 0.9204 (p) REVERT: A 219 ILE cc_start: 0.9244 (mm) cc_final: 0.9035 (mm) REVERT: A 229 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8210 (ttm170) REVERT: A 248 SER cc_start: 0.9566 (t) cc_final: 0.9321 (p) REVERT: A 449 GLN cc_start: 0.9369 (mt0) cc_final: 0.8919 (mp10) REVERT: A 451 GLU cc_start: 0.8890 (pt0) cc_final: 0.8320 (pp20) REVERT: A 456 MET cc_start: 0.8146 (pmm) cc_final: 0.7936 (pmm) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1906 time to fit residues: 60.9122 Evaluate side-chains 185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 9 optimal weight: 0.0670 chunk 60 optimal weight: 0.0000 chunk 66 optimal weight: 5.9990 overall best weight: 0.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.115622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092434 restraints weight = 29929.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.095289 restraints weight = 20511.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.097349 restraints weight = 15302.553| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8950 Z= 0.118 Angle : 0.655 12.066 12092 Z= 0.328 Chirality : 0.042 0.236 1440 Planarity : 0.004 0.036 1532 Dihedral : 4.855 21.479 1238 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1134 helix: 0.54 (0.20), residues: 662 sheet: -0.49 (0.70), residues: 57 loop : -1.98 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 91 HIS 0.005 0.001 HIS B 576 PHE 0.024 0.001 PHE B 319 TYR 0.011 0.001 TYR A 87 ARG 0.003 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 478) hydrogen bonds : angle 4.55155 ( 1404) covalent geometry : bond 0.00237 ( 8950) covalent geometry : angle 0.65505 (12092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.9385 (mt) cc_final: 0.9166 (mt) REVERT: B 47 LEU cc_start: 0.8995 (mt) cc_final: 0.8606 (mt) REVERT: B 124 LEU cc_start: 0.9583 (tp) cc_final: 0.9380 (tp) REVERT: B 132 SER cc_start: 0.9478 (t) cc_final: 0.9122 (p) REVERT: B 133 GLU cc_start: 0.8306 (mp0) cc_final: 0.7804 (mp0) REVERT: B 229 ARG cc_start: 0.8791 (ttm170) cc_final: 0.8528 (ttm170) REVERT: B 316 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8937 (tp-100) REVERT: B 393 TYR cc_start: 0.6697 (m-80) cc_final: 0.6428 (m-80) REVERT: B 430 ASN cc_start: 0.7831 (p0) cc_final: 0.7211 (p0) REVERT: B 456 MET cc_start: 0.9140 (mpp) cc_final: 0.8818 (mmm) REVERT: A 44 MET cc_start: 0.8958 (tmm) cc_final: 0.8579 (tmm) REVERT: A 45 LEU cc_start: 0.9450 (mt) cc_final: 0.9131 (mt) REVERT: A 126 SER cc_start: 0.9457 (m) cc_final: 0.9220 (p) REVERT: A 219 ILE cc_start: 0.9262 (mm) cc_final: 0.9058 (mm) REVERT: A 229 ARG cc_start: 0.8505 (tpp80) cc_final: 0.8194 (tpp80) REVERT: A 248 SER cc_start: 0.9563 (t) cc_final: 0.9325 (p) REVERT: A 449 GLN cc_start: 0.9380 (mt0) cc_final: 0.8920 (mp10) REVERT: A 451 GLU cc_start: 0.8896 (pt0) cc_final: 0.8316 (pp20) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1935 time to fit residues: 61.9010 Evaluate side-chains 190 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** A 197 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 = 0.3933 r_free = 0.3933 target = 0.112030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.088973 restraints weight = 31630.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091533 restraints weight = 22339.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.093435 restraints weight = 17154.440| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8950 Z= 0.147 Angle : 0.657 8.697 12092 Z= 0.339 Chirality : 0.043 0.200 1440 Planarity : 0.004 0.033 1532 Dihedral : 4.957 21.696 1238 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.10 % Allowed : 2.69 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1134 helix: 0.48 (0.20), residues: 667 sheet: 0.20 (0.80), residues: 40 loop : -1.90 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 91 HIS 0.005 0.001 HIS B 576 PHE 0.018 0.002 PHE B 319 TYR 0.010 0.001 TYR B 268 ARG 0.003 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 478) hydrogen bonds : angle 4.58872 ( 1404) covalent geometry : bond 0.00299 ( 8950) covalent geometry : angle 0.65651 (12092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.9413 (mt) cc_final: 0.9145 (mt) REVERT: B 47 LEU cc_start: 0.9035 (mt) cc_final: 0.8711 (mt) REVERT: B 132 SER cc_start: 0.9495 (t) cc_final: 0.9154 (p) REVERT: B 133 GLU cc_start: 0.8301 (mp0) cc_final: 0.7759 (mp0) REVERT: B 229 ARG cc_start: 0.8759 (ttm170) cc_final: 0.8361 (ttm170) REVERT: B 312 MET cc_start: 0.5628 (tpp) cc_final: 0.4608 (tpp) REVERT: B 430 ASN cc_start: 0.8111 (p0) cc_final: 0.7592 (p0) REVERT: B 431 ASP cc_start: 0.7535 (t0) cc_final: 0.7165 (t0) REVERT: B 456 MET cc_start: 0.9137 (mpp) cc_final: 0.8800 (mmm) REVERT: A 44 MET cc_start: 0.9009 (tmm) cc_final: 0.8661 (tmm) REVERT: A 45 LEU cc_start: 0.9455 (mt) cc_final: 0.9119 (mt) REVERT: A 126 SER cc_start: 0.9493 (m) cc_final: 0.9266 (p) REVERT: A 219 ILE cc_start: 0.9279 (mm) cc_final: 0.9056 (mm) REVERT: A 229 ARG cc_start: 0.8691 (tpp80) cc_final: 0.8341 (tpp80) REVERT: A 248 SER cc_start: 0.9573 (t) cc_final: 0.9332 (p) REVERT: A 312 MET cc_start: 0.4868 (ttt) cc_final: 0.4565 (tpt) REVERT: A 359 LEU cc_start: 0.7679 (mp) cc_final: 0.7442 (pt) REVERT: A 449 GLN cc_start: 0.9377 (mt0) cc_final: 0.8991 (mp10) outliers start: 1 outliers final: 1 residues processed: 225 average time/residue: 0.1849 time to fit residues: 58.6172 Evaluate side-chains 181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 527 GLN ** A 197 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 = 0.3941 r_free = 0.3941 target = 0.112566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089412 restraints weight = 32590.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.091983 restraints weight = 23134.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.093915 restraints weight = 17788.867| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8950 Z= 0.137 Angle : 0.685 9.059 12092 Z= 0.351 Chirality : 0.043 0.212 1440 Planarity : 0.004 0.034 1532 Dihedral : 5.013 21.834 1238 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1134 helix: 0.46 (0.20), residues: 665 sheet: 0.32 (0.83), residues: 40 loop : -1.90 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 91 HIS 0.005 0.001 HIS B 576 PHE 0.018 0.002 PHE A 23 TYR 0.011 0.001 TYR A 439 ARG 0.005 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 478) hydrogen bonds : angle 4.63528 ( 1404) covalent geometry : bond 0.00286 ( 8950) covalent geometry : angle 0.68505 (12092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.9401 (mt) cc_final: 0.9143 (mt) REVERT: B 47 LEU cc_start: 0.9006 (mt) cc_final: 0.8711 (mt) REVERT: B 75 MET cc_start: 0.9187 (ttp) cc_final: 0.8865 (ttt) REVERT: B 98 MET cc_start: 0.8248 (tpt) cc_final: 0.7621 (tmm) REVERT: B 132 SER cc_start: 0.9505 (t) cc_final: 0.9162 (p) REVERT: B 133 GLU cc_start: 0.8310 (mp0) cc_final: 0.7757 (mp0) REVERT: B 312 MET cc_start: 0.5738 (tpp) cc_final: 0.5302 (tpp) REVERT: B 456 MET cc_start: 0.9130 (mpp) cc_final: 0.8842 (mpp) REVERT: A 44 MET cc_start: 0.8986 (tmm) cc_final: 0.8614 (tmm) REVERT: A 126 SER cc_start: 0.9492 (m) cc_final: 0.9264 (p) REVERT: A 219 ILE cc_start: 0.9263 (mm) cc_final: 0.9052 (mm) REVERT: A 229 ARG cc_start: 0.8670 (tpp80) cc_final: 0.8444 (tpp80) REVERT: A 248 SER cc_start: 0.9583 (t) cc_final: 0.9352 (p) REVERT: A 359 LEU cc_start: 0.7512 (mp) cc_final: 0.7292 (pp) REVERT: A 449 GLN cc_start: 0.9351 (mt0) cc_final: 0.8985 (mp10) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1739 time to fit residues: 55.3255 Evaluate side-chains 180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.111311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.088115 restraints weight = 30855.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.090899 restraints weight = 20859.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.092940 restraints weight = 15504.656| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8950 Z= 0.127 Angle : 0.681 8.550 12092 Z= 0.346 Chirality : 0.043 0.221 1440 Planarity : 0.004 0.034 1532 Dihedral : 4.953 21.954 1238 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1134 helix: 0.53 (0.20), residues: 664 sheet: 0.41 (0.85), residues: 40 loop : -1.86 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 91 HIS 0.005 0.001 HIS B 576 PHE 0.018 0.001 PHE A 23 TYR 0.009 0.001 TYR A 572 ARG 0.003 0.000 ARG A 441 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 478) hydrogen bonds : angle 4.59481 ( 1404) covalent geometry : bond 0.00266 ( 8950) covalent geometry : angle 0.68122 (12092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.9398 (mt) cc_final: 0.9156 (mt) REVERT: B 47 LEU cc_start: 0.8980 (mt) cc_final: 0.8668 (mt) REVERT: B 75 MET cc_start: 0.9256 (ttp) cc_final: 0.8977 (ttt) REVERT: B 98 MET cc_start: 0.8321 (tpt) cc_final: 0.7745 (tmm) REVERT: B 109 MET cc_start: 0.8585 (mmp) cc_final: 0.8319 (mmp) REVERT: B 132 SER cc_start: 0.9512 (t) cc_final: 0.9168 (p) REVERT: B 133 GLU cc_start: 0.8337 (mp0) cc_final: 0.7786 (mp0) REVERT: B 312 MET cc_start: 0.5604 (tpp) cc_final: 0.5284 (tpp) REVERT: B 430 ASN cc_start: 0.7931 (p0) cc_final: 0.7330 (p0) REVERT: B 431 ASP cc_start: 0.7464 (t0) cc_final: 0.6893 (t0) REVERT: B 456 MET cc_start: 0.9192 (mpp) cc_final: 0.8874 (mpp) REVERT: A 44 MET cc_start: 0.9055 (tmm) cc_final: 0.8661 (tmm) REVERT: A 126 SER cc_start: 0.9529 (m) cc_final: 0.9309 (p) REVERT: A 157 PHE cc_start: 0.8566 (t80) cc_final: 0.8336 (t80) REVERT: A 229 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8305 (ttm170) REVERT: A 248 SER cc_start: 0.9582 (t) cc_final: 0.9346 (p) REVERT: A 449 GLN cc_start: 0.9390 (mt0) cc_final: 0.9035 (mp10) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1727 time to fit residues: 55.1011 Evaluate side-chains 184 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 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 = 0.3935 r_free = 0.3935 target = 0.112309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088850 restraints weight = 30711.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.091599 restraints weight = 21064.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.093653 restraints weight = 15778.149| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8950 Z= 0.127 Angle : 0.689 8.285 12092 Z= 0.349 Chirality : 0.043 0.220 1440 Planarity : 0.004 0.035 1532 Dihedral : 4.872 22.844 1238 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1134 helix: 0.55 (0.20), residues: 665 sheet: 0.46 (0.86), residues: 40 loop : -1.85 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 91 HIS 0.005 0.001 HIS B 576 PHE 0.017 0.001 PHE A 23 TYR 0.015 0.001 TYR B 439 ARG 0.006 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 478) hydrogen bonds : angle 4.56436 ( 1404) covalent geometry : bond 0.00266 ( 8950) covalent geometry : angle 0.68898 (12092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.9387 (mt) cc_final: 0.9150 (mt) REVERT: B 47 LEU cc_start: 0.8969 (mt) cc_final: 0.8660 (mt) REVERT: B 75 MET cc_start: 0.9269 (ttp) cc_final: 0.9008 (ttt) REVERT: B 98 MET cc_start: 0.8282 (tpt) cc_final: 0.7795 (tmm) REVERT: B 132 SER cc_start: 0.9541 (t) cc_final: 0.9198 (p) REVERT: B 133 GLU cc_start: 0.8378 (mp0) cc_final: 0.7828 (mp0) REVERT: B 312 MET cc_start: 0.5653 (tpp) cc_final: 0.5265 (tpp) REVERT: B 430 ASN cc_start: 0.7933 (p0) cc_final: 0.7448 (p0) REVERT: B 456 MET cc_start: 0.9200 (mpp) cc_final: 0.8879 (mpp) REVERT: A 44 MET cc_start: 0.9035 (tmm) cc_final: 0.8636 (tmm) REVERT: A 126 SER cc_start: 0.9540 (m) cc_final: 0.9334 (p) REVERT: A 157 PHE cc_start: 0.8555 (t80) cc_final: 0.8327 (t80) REVERT: A 229 ARG cc_start: 0.8742 (tpp80) cc_final: 0.8439 (tpp80) REVERT: A 248 SER cc_start: 0.9577 (t) cc_final: 0.9345 (p) REVERT: A 449 GLN cc_start: 0.9384 (mt0) cc_final: 0.9039 (mp10) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1871 time to fit residues: 58.7788 Evaluate side-chains 180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.113699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090500 restraints weight = 31617.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.093086 restraints weight = 22313.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.095035 restraints weight = 17148.504| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8950 Z= 0.125 Angle : 0.693 8.366 12092 Z= 0.348 Chirality : 0.043 0.234 1440 Planarity : 0.004 0.038 1532 Dihedral : 4.874 23.131 1238 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1134 helix: 0.59 (0.20), residues: 665 sheet: 1.43 (1.02), residues: 30 loop : -1.81 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 91 HIS 0.005 0.001 HIS B 576 PHE 0.017 0.001 PHE A 23 TYR 0.009 0.001 TYR B 393 ARG 0.006 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 478) hydrogen bonds : angle 4.53311 ( 1404) covalent geometry : bond 0.00261 ( 8950) covalent geometry : angle 0.69336 (12092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.9369 (mt) cc_final: 0.9137 (mt) REVERT: B 47 LEU cc_start: 0.8953 (mt) cc_final: 0.8643 (mt) REVERT: B 98 MET cc_start: 0.8318 (tpt) cc_final: 0.7842 (tmm) REVERT: B 109 MET cc_start: 0.8523 (mmp) cc_final: 0.8266 (mmp) REVERT: B 124 LEU cc_start: 0.9547 (tp) cc_final: 0.9339 (tp) REVERT: B 132 SER cc_start: 0.9550 (t) cc_final: 0.9247 (p) REVERT: B 133 GLU cc_start: 0.8387 (mp0) cc_final: 0.7891 (mp0) REVERT: B 312 MET cc_start: 0.5607 (tpp) cc_final: 0.3185 (tpp) REVERT: B 316 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8709 (mm-40) REVERT: B 430 ASN cc_start: 0.7880 (p0) cc_final: 0.7515 (p0) REVERT: B 456 MET cc_start: 0.9224 (mpp) cc_final: 0.8900 (mpp) REVERT: A 44 MET cc_start: 0.8987 (tmm) cc_final: 0.8604 (tmm) REVERT: A 126 SER cc_start: 0.9529 (m) cc_final: 0.9320 (p) REVERT: A 157 PHE cc_start: 0.8529 (t80) cc_final: 0.8122 (t80) REVERT: A 229 ARG cc_start: 0.8737 (tpp80) cc_final: 0.8464 (tpp80) REVERT: A 248 SER cc_start: 0.9558 (t) cc_final: 0.9327 (p) REVERT: A 312 MET cc_start: 0.4719 (ttt) cc_final: 0.4227 (tpt) REVERT: A 449 GLN cc_start: 0.9374 (mt0) cc_final: 0.9043 (mp10) REVERT: A 488 ARG cc_start: 0.8499 (ttt180) cc_final: 0.8084 (ttt180) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1843 time to fit residues: 57.0759 Evaluate side-chains 183 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 0.0270 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 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 = 0.3896 r_free = 0.3896 target = 0.109725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.086294 restraints weight = 30890.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.088937 restraints weight = 21292.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.090816 restraints weight = 16008.699| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8950 Z= 0.151 Angle : 0.707 9.541 12092 Z= 0.360 Chirality : 0.044 0.230 1440 Planarity : 0.004 0.035 1532 Dihedral : 4.944 23.575 1238 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.26), residues: 1134 helix: 0.56 (0.20), residues: 664 sheet: 1.38 (1.03), residues: 30 loop : -1.72 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 91 HIS 0.006 0.001 HIS B 576 PHE 0.018 0.002 PHE A 23 TYR 0.009 0.001 TYR B 268 ARG 0.007 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 478) hydrogen bonds : angle 4.62588 ( 1404) covalent geometry : bond 0.00315 ( 8950) covalent geometry : angle 0.70703 (12092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3193.34 seconds wall clock time: 56 minutes 42.05 seconds (3402.05 seconds total)