Starting phenix.real_space_refine on Fri Nov 15 03:40:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8z_42030/11_2024/8u8z_42030.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8z_42030/11_2024/8u8z_42030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8z_42030/11_2024/8u8z_42030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8z_42030/11_2024/8u8z_42030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8z_42030/11_2024/8u8z_42030.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8z_42030/11_2024/8u8z_42030.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 46 5.16 5 C 5129 2.51 5 N 1431 2.21 5 O 1541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8147 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4031 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4030 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.84, per 1000 atoms: 0.72 Number of scatterers: 8147 At special positions: 0 Unit cell: (101.178, 81.468, 129.429, 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 46 16.00 O 1541 8.00 N 1431 7.00 C 5129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 379 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 45.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 49 through 52 Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.538A pdb=" N GLY A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.024A pdb=" N ARG A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 133' Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.900A pdb=" N ARG A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 294 through 340 removed outlier: 4.304A pdb=" N GLN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.597A pdb=" N LEU A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 396 removed outlier: 4.021A pdb=" N ALA A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 395 " --> pdb=" O TRP A 391 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 396 " --> pdb=" O MET A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.933A pdb=" N VAL A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.643A pdb=" N GLU A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 414 " --> pdb=" O PRO A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 488 through 516 Processing helix chain 'A' and resid 517 through 534 removed outlier: 3.513A pdb=" N ARG A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 534 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.515A pdb=" N ASP B 18 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 52 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.920A pdb=" N ARG B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 133' Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 148 through 165 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.520A pdb=" N ILE B 204 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.874A pdb=" N ARG B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 294 through 340 removed outlier: 4.462A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.648A pdb=" N LEU B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.957A pdb=" N ALA B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY B 395 " --> pdb=" O TRP B 391 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.952A pdb=" N VAL B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.607A pdb=" N GLU B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 414 " --> pdb=" O PRO B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 488 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.533A pdb=" N VAL A 46 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 33 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU A 101 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.578A pdb=" N GLY A 180 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 185 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A 169 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP A 280 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN A 275 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 281 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 269 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 377 Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 449 removed outlier: 3.853A pdb=" N GLN A 444 " --> pdb=" O MET A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.197A pdb=" N ILE B 43 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS B 37 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 33 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.563A pdb=" N GLY B 180 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 171 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 185 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 169 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP B 280 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU B 279 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN B 275 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 281 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET B 269 " --> pdb=" O CYS B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 377 Processing sheet with id=AA8, first strand: chain 'B' and resid 444 through 449 removed outlier: 4.007A pdb=" N GLN B 444 " --> pdb=" O MET B 480 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1260 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: 2.58 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1516 1.33 - 1.45: 2006 1.45 - 1.57: 4713 1.57 - 1.69: 0 1.69 - 1.82: 78 Bond restraints: 8313 Sorted by residual: bond pdb=" CB THR A 35 " pdb=" CG2 THR A 35 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CB ARG B 138 " pdb=" CG ARG B 138 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.96e+00 bond pdb=" CB VAL A 431 " pdb=" CG1 VAL A 431 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 bond pdb=" CG LEU A 117 " pdb=" CD1 LEU A 117 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" CB GLN B 372 " pdb=" CG GLN B 372 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.31e+00 ... (remaining 8308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 11018 1.87 - 3.74: 239 3.74 - 5.61: 39 5.61 - 7.48: 8 7.48 - 9.35: 1 Bond angle restraints: 11305 Sorted by residual: angle pdb=" CA GLN B 372 " pdb=" CB GLN B 372 " pdb=" CG GLN B 372 " ideal model delta sigma weight residual 114.10 120.52 -6.42 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N MET B 136 " pdb=" CA MET B 136 " pdb=" C MET B 136 " ideal model delta sigma weight residual 111.03 114.26 -3.23 1.11e+00 8.12e-01 8.49e+00 angle pdb=" CB GLN B 372 " pdb=" CG GLN B 372 " pdb=" CD GLN B 372 " ideal model delta sigma weight residual 112.60 117.29 -4.69 1.70e+00 3.46e-01 7.61e+00 angle pdb=" CA CYS B 375 " pdb=" CB CYS B 375 " pdb=" SG CYS B 375 " ideal model delta sigma weight residual 114.40 108.10 6.30 2.30e+00 1.89e-01 7.51e+00 angle pdb=" CA LEU A 115 " pdb=" CB LEU A 115 " pdb=" CG LEU A 115 " ideal model delta sigma weight residual 116.30 125.65 -9.35 3.50e+00 8.16e-02 7.13e+00 ... (remaining 11300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4283 17.14 - 34.28: 536 34.28 - 51.43: 181 51.43 - 68.57: 55 68.57 - 85.71: 8 Dihedral angle restraints: 5063 sinusoidal: 2065 harmonic: 2998 Sorted by residual: dihedral pdb=" CB CYS B 375 " pdb=" SG CYS B 375 " pdb=" SG CYS B 379 " pdb=" CB CYS B 379 " ideal model delta sinusoidal sigma weight residual 93.00 45.23 47.77 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CB CYS A 375 " pdb=" SG CYS A 375 " pdb=" SG CYS A 379 " pdb=" CB CYS A 379 " ideal model delta sinusoidal sigma weight residual -86.00 -54.14 -31.86 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CA ASP A 347 " pdb=" CB ASP A 347 " pdb=" CG ASP A 347 " pdb=" OD1 ASP A 347 " ideal model delta sinusoidal sigma weight residual -30.00 -89.68 59.68 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 5060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 920 0.042 - 0.084: 226 0.084 - 0.126: 104 0.126 - 0.168: 17 0.168 - 0.210: 2 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA ARG B 138 " pdb=" N ARG B 138 " pdb=" C ARG B 138 " pdb=" CB ARG B 138 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 155 " pdb=" CA VAL A 155 " pdb=" CG1 VAL A 155 " pdb=" CG2 VAL A 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU A 106 " pdb=" CB LEU A 106 " pdb=" CD1 LEU A 106 " pdb=" CD2 LEU A 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1266 not shown) Planarity restraints: 1479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 493 " -0.016 2.00e-02 2.50e+03 2.90e-02 1.47e+01 pdb=" CG PHE A 493 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 493 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 493 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 493 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 493 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 493 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 427 " -0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO A 428 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 427 " -0.056 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO B 428 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " -0.047 5.00e-02 4.00e+02 ... (remaining 1476 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 86 2.65 - 3.21: 7253 3.21 - 3.77: 12656 3.77 - 4.34: 16846 4.34 - 4.90: 28281 Nonbonded interactions: 65122 Sorted by model distance: nonbonded pdb=" OD1 ASN B 135 " pdb=" NH1 ARG B 138 " model vdw 2.082 3.120 nonbonded pdb=" OE1 GLU B 118 " pdb=" OH TYR B 292 " model vdw 2.159 3.040 nonbonded pdb=" OD2 ASP B 203 " pdb=" OH TYR B 259 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 341 " pdb=" OG1 THR A 343 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR B 238 " pdb=" OE1 GLN B 240 " model vdw 2.237 3.040 ... (remaining 65117 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 533 or resid 900)) selection = (chain 'B' and (resid 12 through 533 or resid 900)) } 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 individual isotropic 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: 3.240 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.960 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.003 0.061 8313 Z= 0.192 Angle : 0.657 9.347 11305 Z= 0.343 Chirality : 0.046 0.210 1269 Planarity : 0.006 0.090 1479 Dihedral : 17.592 85.710 3113 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.91 % Allowed : 28.57 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.97 (0.27), residues: 1026 helix: 2.04 (0.26), residues: 405 sheet: -0.23 (0.37), residues: 198 loop : -0.23 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 476 HIS 0.007 0.001 HIS A 107 PHE 0.061 0.002 PHE A 493 TYR 0.026 0.002 TYR B 212 ARG 0.010 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8402 (mp) cc_final: 0.7737 (mp) REVERT: A 337 MET cc_start: 0.8019 (ttp) cc_final: 0.7790 (ttt) outliers start: 8 outliers final: 2 residues processed: 106 average time/residue: 0.2165 time to fit residues: 31.8036 Evaluate side-chains 63 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 69 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8313 Z= 0.224 Angle : 0.569 6.560 11305 Z= 0.295 Chirality : 0.042 0.132 1269 Planarity : 0.005 0.053 1479 Dihedral : 6.456 67.597 1166 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.63 % Allowed : 24.72 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.69 (0.27), residues: 1026 helix: 1.72 (0.25), residues: 408 sheet: -0.23 (0.38), residues: 194 loop : -0.38 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.004 0.001 HIS A 30 PHE 0.017 0.001 PHE A 34 TYR 0.011 0.001 TYR A 259 ARG 0.007 0.001 ARG A 521 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.9184 (m) cc_final: 0.8929 (t) REVERT: A 116 GLU cc_start: 0.8046 (pm20) cc_final: 0.7845 (pm20) outliers start: 32 outliers final: 9 residues processed: 96 average time/residue: 0.1834 time to fit residues: 25.2854 Evaluate side-chains 65 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 471 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.0040 chunk 28 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8313 Z= 0.306 Angle : 0.572 5.803 11305 Z= 0.298 Chirality : 0.043 0.178 1269 Planarity : 0.004 0.042 1479 Dihedral : 6.264 58.553 1162 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.29 % Allowed : 24.60 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.61 (0.26), residues: 1026 helix: 1.63 (0.25), residues: 411 sheet: -0.15 (0.38), residues: 184 loop : -0.48 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.015 0.002 PHE A 34 TYR 0.010 0.001 TYR A 259 ARG 0.008 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 191 MET cc_start: 0.8427 (tpp) cc_final: 0.7999 (tpt) outliers start: 29 outliers final: 17 residues processed: 93 average time/residue: 0.1718 time to fit residues: 23.4457 Evaluate side-chains 71 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 GLN B 233 GLN B 241 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8313 Z= 0.180 Angle : 0.522 7.415 11305 Z= 0.269 Chirality : 0.041 0.169 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.148 56.427 1162 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.29 % Allowed : 24.38 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.69 (0.26), residues: 1026 helix: 1.71 (0.25), residues: 411 sheet: -0.04 (0.38), residues: 182 loop : -0.49 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.010 0.001 PHE A 34 TYR 0.013 0.001 TYR B 292 ARG 0.003 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8856 (mm) cc_final: 0.8656 (mp) REVERT: A 337 MET cc_start: 0.8041 (ttp) cc_final: 0.7574 (ptm) REVERT: B 191 MET cc_start: 0.8390 (tpp) cc_final: 0.7910 (tpp) outliers start: 29 outliers final: 14 residues processed: 88 average time/residue: 0.1933 time to fit residues: 24.2902 Evaluate side-chains 72 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS B 336 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8313 Z= 0.241 Angle : 0.561 6.794 11305 Z= 0.286 Chirality : 0.042 0.173 1269 Planarity : 0.004 0.036 1479 Dihedral : 6.192 57.094 1162 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.85 % Allowed : 23.81 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.67 (0.26), residues: 1026 helix: 1.76 (0.25), residues: 411 sheet: -0.05 (0.38), residues: 183 loop : -0.57 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.004 0.001 HIS B 295 PHE 0.009 0.001 PHE A 34 TYR 0.009 0.001 TYR B 292 ARG 0.006 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 56 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.8606 (tmm) cc_final: 0.8286 (tmm) REVERT: A 337 MET cc_start: 0.8085 (ttp) cc_final: 0.7641 (ptm) REVERT: B 191 MET cc_start: 0.8384 (tpp) cc_final: 0.7913 (tpp) outliers start: 34 outliers final: 23 residues processed: 87 average time/residue: 0.1850 time to fit residues: 23.2816 Evaluate side-chains 78 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 503 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8313 Z= 0.192 Angle : 0.545 6.419 11305 Z= 0.277 Chirality : 0.042 0.175 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.146 57.791 1162 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.06 % Allowed : 24.94 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.72 (0.26), residues: 1026 helix: 1.83 (0.25), residues: 411 sheet: -0.02 (0.38), residues: 182 loop : -0.57 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS B 30 PHE 0.008 0.001 PHE A 34 TYR 0.008 0.001 TYR A 259 ARG 0.004 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.8601 (tmm) cc_final: 0.8358 (tmm) REVERT: A 337 MET cc_start: 0.8066 (ttp) cc_final: 0.7627 (ptm) REVERT: B 93 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8181 (mp) REVERT: B 191 MET cc_start: 0.8369 (tpp) cc_final: 0.7938 (tpp) outliers start: 27 outliers final: 20 residues processed: 83 average time/residue: 0.2038 time to fit residues: 24.1108 Evaluate side-chains 72 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 503 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8313 Z= 0.206 Angle : 0.544 6.751 11305 Z= 0.277 Chirality : 0.042 0.181 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.136 58.885 1162 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.20 % Allowed : 23.92 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.73 (0.26), residues: 1026 helix: 1.84 (0.25), residues: 416 sheet: 0.03 (0.38), residues: 182 loop : -0.63 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS B 30 PHE 0.008 0.001 PHE A 34 TYR 0.012 0.001 TYR A 259 ARG 0.002 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 52 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8541 (tp) REVERT: A 139 MET cc_start: 0.8625 (tmm) cc_final: 0.8392 (tmm) REVERT: A 337 MET cc_start: 0.8076 (ttp) cc_final: 0.7673 (ptm) REVERT: A 521 ARG cc_start: 0.8648 (mtp180) cc_final: 0.8294 (mtt90) REVERT: B 93 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8180 (mp) outliers start: 37 outliers final: 29 residues processed: 86 average time/residue: 0.1970 time to fit residues: 24.2323 Evaluate side-chains 81 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 50 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 503 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.0870 chunk 62 optimal weight: 8.9990 chunk 66 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 94 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8313 Z= 0.153 Angle : 0.533 7.472 11305 Z= 0.269 Chirality : 0.041 0.180 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.017 57.264 1162 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.49 % Allowed : 25.28 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.76 (0.26), residues: 1026 helix: 1.89 (0.25), residues: 404 sheet: 0.13 (0.38), residues: 181 loop : -0.62 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 476 HIS 0.003 0.001 HIS B 30 PHE 0.014 0.001 PHE B 23 TYR 0.012 0.001 TYR A 259 ARG 0.002 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 337 MET cc_start: 0.8040 (ttp) cc_final: 0.7666 (ptm) REVERT: A 521 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8260 (mtt90) outliers start: 22 outliers final: 18 residues processed: 77 average time/residue: 0.1975 time to fit residues: 22.3526 Evaluate side-chains 68 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 503 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 60 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8313 Z= 0.203 Angle : 0.555 10.007 11305 Z= 0.278 Chirality : 0.042 0.174 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.066 59.056 1162 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.27 % Allowed : 25.74 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.80 (0.26), residues: 1026 helix: 1.92 (0.25), residues: 410 sheet: 0.13 (0.38), residues: 182 loop : -0.61 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 30 PHE 0.008 0.001 PHE A 34 TYR 0.012 0.001 TYR A 259 ARG 0.004 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.900 Fit side-chains REVERT: A 337 MET cc_start: 0.8074 (ttp) cc_final: 0.7741 (ptm) outliers start: 20 outliers final: 18 residues processed: 68 average time/residue: 0.1754 time to fit residues: 17.9079 Evaluate side-chains 68 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 503 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.0020 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8313 Z= 0.271 Angle : 0.587 8.280 11305 Z= 0.297 Chirality : 0.043 0.174 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.227 58.795 1162 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.27 % Allowed : 25.40 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.74 (0.26), residues: 1026 helix: 1.87 (0.25), residues: 416 sheet: -0.03 (0.37), residues: 184 loop : -0.61 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.004 0.001 HIS A 30 PHE 0.010 0.001 PHE A 34 TYR 0.011 0.001 TYR A 259 ARG 0.004 0.000 ARG B 519 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 1.021 Fit side-chains REVERT: A 337 MET cc_start: 0.8110 (ttp) cc_final: 0.7708 (ptm) outliers start: 20 outliers final: 19 residues processed: 71 average time/residue: 0.1852 time to fit residues: 19.2601 Evaluate side-chains 66 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.0050 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 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 = 0.3586 r_free = 0.3586 target = 0.079892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060786 restraints weight = 24130.462| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.15 r_work: 0.3049 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8313 Z= 0.165 Angle : 0.572 9.747 11305 Z= 0.284 Chirality : 0.042 0.175 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.081 57.716 1162 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.04 % Allowed : 26.19 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.70 (0.27), residues: 1026 helix: 1.82 (0.25), residues: 404 sheet: -0.02 (0.36), residues: 193 loop : -0.58 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.003 0.001 HIS A 107 PHE 0.007 0.001 PHE A 102 TYR 0.011 0.001 TYR A 259 ARG 0.005 0.000 ARG A 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.71 seconds wall clock time: 38 minutes 41.87 seconds (2321.87 seconds total)