Starting phenix.real_space_refine on Fri Jun 6 21:26:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8z_42030/06_2025/8u8z_42030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8z_42030/06_2025/8u8z_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/cci-nas-00/data/ceres_data/8u8z_42030/06_2025/8u8z_42030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8z_42030/06_2025/8u8z_42030.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8z_42030/06_2025/8u8z_42030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8z_42030/06_2025/8u8z_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-5710/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: 6.11, per 1000 atoms: 0.75 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: 2.46 Conformation dependent library (CDL) restraints added in 1.0 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: 0.93 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: 2.50 Time building geometry restraints manager: 2.86 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: 6.080 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.820 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.670 ------------------------------------------------------------------------------- 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 0.066 8317 Z= 0.167 Angle : 0.659 9.347 11309 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 Details of bonding type rmsd hydrogen bonds : bond 0.14626 ( 445) hydrogen bonds : angle 5.63865 ( 1260) SS BOND : bond 0.00187 ( 2) SS BOND : angle 2.93532 ( 4) covalent geometry : bond 0.00304 ( 8313) covalent geometry : angle 0.65654 (11305) Misc. bond : bond 0.06518 ( 2) *********************** 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 : 0.960 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: 0.1997 time to fit residues: 29.3209 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 : 0.924 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.081356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061695 restraints weight = 23748.193| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 4.30 r_work: 0.2997 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 8317 Z= 0.149 Angle : 0.569 6.560 11309 Z= 0.295 Chirality : 0.042 0.132 1269 Planarity : 0.005 0.053 1479 Dihedral : 6.456 67.598 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 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 445) hydrogen bonds : angle 4.80474 ( 1260) SS BOND : bond 0.00353 ( 2) SS BOND : angle 0.89997 ( 4) covalent geometry : bond 0.00339 ( 8313) covalent geometry : angle 0.56855 (11305) Misc. bond : bond 0.00083 ( 2) *********************** 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 : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8123 (pm20) cc_final: 0.7794 (pm20) REVERT: A 328 ILE cc_start: 0.9657 (OUTLIER) cc_final: 0.9435 (mt) REVERT: A 451 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7566 (t70) REVERT: A 476 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.7918 (t60) REVERT: A 480 MET cc_start: 0.9090 (mmm) cc_final: 0.8754 (mmp) REVERT: B 40 GLU cc_start: 0.8101 (tp30) cc_final: 0.7662 (tp30) outliers start: 32 outliers final: 9 residues processed: 96 average time/residue: 0.1802 time to fit residues: 25.0777 Evaluate side-chains 69 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 A residue 328 ILE Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP 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 15 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 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 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061242 restraints weight = 24366.079| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.25 r_work: 0.3013 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8317 Z= 0.120 Angle : 0.517 6.663 11309 Z= 0.268 Chirality : 0.041 0.169 1269 Planarity : 0.004 0.042 1479 Dihedral : 6.039 57.690 1162 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.38 % Allowed : 25.51 % 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: 0.65 (0.26), residues: 1026 helix: 1.68 (0.25), residues: 410 sheet: -0.19 (0.37), residues: 192 loop : -0.44 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.011 0.001 PHE A 34 TYR 0.009 0.001 TYR A 259 ARG 0.006 0.000 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 445) hydrogen bonds : angle 4.64957 ( 1260) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.63255 ( 4) covalent geometry : bond 0.00266 ( 8313) covalent geometry : angle 0.51716 (11305) Misc. bond : bond 0.00135 ( 2) *********************** 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 88 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.8233 (pm20) cc_final: 0.7818 (pm20) REVERT: A 316 GLU cc_start: 0.9190 (tp30) cc_final: 0.8938 (tp30) REVERT: A 328 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9417 (mt) REVERT: A 476 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: A 480 MET cc_start: 0.9138 (mmm) cc_final: 0.8849 (mmp) REVERT: B 40 GLU cc_start: 0.8077 (tp30) cc_final: 0.7812 (tp30) REVERT: B 191 MET cc_start: 0.8760 (tpp) cc_final: 0.8471 (tpt) outliers start: 21 outliers final: 10 residues processed: 87 average time/residue: 0.2050 time to fit residues: 26.2849 Evaluate side-chains 70 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 228 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 476 TRP 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 476 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 0.0040 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.0996 ------------------------------------------------------------------------------- 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 B 233 GLN B 241 GLN B 295 HIS B 336 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.057555 restraints weight = 24563.339| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 4.15 r_work: 0.2925 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8317 Z= 0.226 Angle : 0.578 6.115 11309 Z= 0.300 Chirality : 0.043 0.139 1269 Planarity : 0.004 0.037 1479 Dihedral : 6.390 57.904 1162 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.99 % Allowed : 22.90 % 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: 0.64 (0.26), residues: 1026 helix: 1.68 (0.25), residues: 415 sheet: -0.10 (0.38), residues: 184 loop : -0.54 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 476 HIS 0.005 0.001 HIS B 144 PHE 0.015 0.002 PHE A 34 TYR 0.016 0.002 TYR B 292 ARG 0.012 0.000 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 445) hydrogen bonds : angle 4.73061 ( 1260) SS BOND : bond 0.00369 ( 2) SS BOND : angle 0.64964 ( 4) covalent geometry : bond 0.00511 ( 8313) covalent geometry : angle 0.57794 (11305) Misc. bond : bond 0.00135 ( 2) *********************** 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 102 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 58 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7769 (pt0) REVERT: A 191 MET cc_start: 0.8438 (tpp) cc_final: 0.7888 (ttm) REVERT: A 328 ILE cc_start: 0.9609 (OUTLIER) cc_final: 0.9365 (mt) REVERT: A 451 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7783 (t70) REVERT: A 476 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7707 (m-10) REVERT: A 480 MET cc_start: 0.9212 (mmm) cc_final: 0.8971 (mmp) REVERT: B 40 GLU cc_start: 0.8154 (tp30) cc_final: 0.7745 (tp30) REVERT: B 191 MET cc_start: 0.8903 (tpp) cc_final: 0.8054 (tpp) REVERT: B 458 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8712 (mm) outliers start: 44 outliers final: 22 residues processed: 97 average time/residue: 0.3085 time to fit residues: 42.7209 Evaluate side-chains 81 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 139 MET 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 328 ILE 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 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 60 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 115 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 471 THR 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 66 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 90 optimal weight: 0.0770 chunk 8 optimal weight: 0.1980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060960 restraints weight = 23689.989| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.95 r_work: 0.2993 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8317 Z= 0.111 Angle : 0.527 6.565 11309 Z= 0.269 Chirality : 0.041 0.177 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.138 55.857 1162 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.29 % Allowed : 24.26 % Favored : 72.45 % 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: 1.81 (0.25), residues: 411 sheet: -0.03 (0.38), residues: 182 loop : -0.56 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.008 0.001 PHE A 34 TYR 0.010 0.001 TYR B 292 ARG 0.007 0.000 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 445) hydrogen bonds : angle 4.55390 ( 1260) SS BOND : bond 0.00722 ( 2) SS BOND : angle 1.49854 ( 4) covalent geometry : bond 0.00245 ( 8313) covalent geometry : angle 0.52673 (11305) Misc. bond : bond 0.00085 ( 2) *********************** 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 91 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: A 116 GLU cc_start: 0.8375 (pm20) cc_final: 0.7907 (pm20) REVERT: A 316 GLU cc_start: 0.9156 (tp30) cc_final: 0.8909 (tp30) REVERT: A 328 ILE cc_start: 0.9599 (OUTLIER) cc_final: 0.9344 (mt) REVERT: A 337 MET cc_start: 0.9014 (ttp) cc_final: 0.8180 (ptm) REVERT: A 451 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7717 (t70) REVERT: A 476 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.7738 (m-10) REVERT: A 480 MET cc_start: 0.9201 (mmm) cc_final: 0.8963 (mmp) REVERT: A 521 ARG cc_start: 0.8718 (mtp180) cc_final: 0.8180 (mtp85) REVERT: B 40 GLU cc_start: 0.8116 (tp30) cc_final: 0.7668 (tp30) REVERT: B 191 MET cc_start: 0.8843 (tpp) cc_final: 0.8083 (tpp) REVERT: B 458 LEU cc_start: 0.9098 (tp) cc_final: 0.8735 (mm) REVERT: B 480 MET cc_start: 0.8605 (tpp) cc_final: 0.8382 (mmm) outliers start: 29 outliers final: 12 residues processed: 89 average time/residue: 0.2231 time to fit residues: 28.8403 Evaluate side-chains 74 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP 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 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 20 optimal weight: 0.1980 chunk 98 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.078330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058881 restraints weight = 24250.903| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.21 r_work: 0.2963 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8317 Z= 0.129 Angle : 0.539 7.498 11309 Z= 0.272 Chirality : 0.041 0.173 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.106 58.128 1162 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.06 % Allowed : 24.49 % Favored : 72.45 % 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: 0.77 (0.26), residues: 1026 helix: 1.89 (0.25), residues: 411 sheet: 0.04 (0.38), residues: 181 loop : -0.60 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.008 0.001 PHE A 34 TYR 0.011 0.001 TYR A 259 ARG 0.005 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 445) hydrogen bonds : angle 4.48178 ( 1260) SS BOND : bond 0.00332 ( 2) SS BOND : angle 1.52019 ( 4) covalent geometry : bond 0.00291 ( 8313) covalent geometry : angle 0.53839 (11305) Misc. bond : bond 0.00082 ( 2) *********************** 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 86 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: A 61 LEU cc_start: 0.8640 (mm) cc_final: 0.8408 (mp) REVERT: A 116 GLU cc_start: 0.8400 (pm20) cc_final: 0.7894 (pm20) REVERT: A 139 MET cc_start: 0.9451 (tmm) cc_final: 0.9067 (tmm) REVERT: A 316 GLU cc_start: 0.9199 (tp30) cc_final: 0.8932 (tp30) REVERT: A 328 ILE cc_start: 0.9587 (OUTLIER) cc_final: 0.9329 (mt) REVERT: A 337 MET cc_start: 0.9050 (ttp) cc_final: 0.8185 (ptm) REVERT: A 451 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7646 (t70) REVERT: A 476 TRP cc_start: 0.8282 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: A 480 MET cc_start: 0.9214 (mmm) cc_final: 0.8981 (mmp) REVERT: B 40 GLU cc_start: 0.8140 (tp30) cc_final: 0.7684 (tp30) REVERT: B 191 MET cc_start: 0.8880 (tpp) cc_final: 0.8145 (tpp) REVERT: B 458 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8758 (mm) outliers start: 27 outliers final: 16 residues processed: 84 average time/residue: 0.2456 time to fit residues: 29.2182 Evaluate side-chains 77 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN 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 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 22 GLN 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 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.077074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.059347 restraints weight = 23864.436| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.95 r_work: 0.2965 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8317 Z= 0.146 Angle : 0.543 6.792 11309 Z= 0.276 Chirality : 0.041 0.168 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.146 59.128 1162 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.40 % Allowed : 24.60 % 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: 0.77 (0.26), residues: 1026 helix: 1.88 (0.25), residues: 416 sheet: 0.02 (0.38), residues: 182 loop : -0.61 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.011 0.001 PHE B 23 TYR 0.012 0.001 TYR A 259 ARG 0.004 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 445) hydrogen bonds : angle 4.47025 ( 1260) SS BOND : bond 0.00599 ( 2) SS BOND : angle 1.86015 ( 4) covalent geometry : bond 0.00331 ( 8313) covalent geometry : angle 0.54224 (11305) Misc. bond : bond 0.00083 ( 2) *********************** 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 84 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 54 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: A 61 LEU cc_start: 0.8668 (mm) cc_final: 0.8441 (mp) REVERT: A 116 GLU cc_start: 0.8445 (pm20) cc_final: 0.7945 (pm20) REVERT: A 139 MET cc_start: 0.9430 (tmm) cc_final: 0.9011 (tmm) REVERT: A 316 GLU cc_start: 0.9191 (tp30) cc_final: 0.8907 (tp30) REVERT: A 328 ILE cc_start: 0.9582 (OUTLIER) cc_final: 0.9321 (mt) REVERT: A 337 MET cc_start: 0.9061 (ttp) cc_final: 0.8225 (ptm) REVERT: A 451 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7666 (t70) REVERT: A 476 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.7727 (m-10) REVERT: A 480 MET cc_start: 0.9218 (mmm) cc_final: 0.8972 (mmp) REVERT: A 521 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8604 (mtp180) REVERT: B 22 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8067 (mm110) REVERT: B 40 GLU cc_start: 0.8138 (tp30) cc_final: 0.7691 (tp30) REVERT: B 93 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8012 (mp) REVERT: B 458 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8755 (mm) outliers start: 30 outliers final: 19 residues processed: 83 average time/residue: 0.2302 time to fit residues: 27.7695 Evaluate side-chains 79 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN 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 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 22 GLN 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 318 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** B 505 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.078799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059954 restraints weight = 24374.592| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 4.06 r_work: 0.3002 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8317 Z= 0.159 Angle : 0.549 7.162 11309 Z= 0.279 Chirality : 0.042 0.181 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.205 59.964 1162 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.51 % Allowed : 24.49 % 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: 0.76 (0.26), residues: 1026 helix: 1.91 (0.25), residues: 416 sheet: -0.08 (0.38), residues: 183 loop : -0.60 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 476 HIS 0.004 0.001 HIS A 30 PHE 0.014 0.001 PHE B 23 TYR 0.011 0.001 TYR A 259 ARG 0.004 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 445) hydrogen bonds : angle 4.46692 ( 1260) SS BOND : bond 0.00344 ( 2) SS BOND : angle 1.55628 ( 4) covalent geometry : bond 0.00361 ( 8313) covalent geometry : angle 0.54880 (11305) Misc. bond : bond 0.00088 ( 2) *********************** 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 86 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8747 (mm) cc_final: 0.8521 (mp) REVERT: A 116 GLU cc_start: 0.8509 (pm20) cc_final: 0.8027 (pm20) REVERT: A 139 MET cc_start: 0.9425 (tmm) cc_final: 0.9139 (tmm) REVERT: A 328 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9329 (mt) REVERT: A 337 MET cc_start: 0.9037 (ttp) cc_final: 0.8247 (ptm) REVERT: A 451 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7673 (t70) REVERT: A 476 TRP cc_start: 0.8369 (OUTLIER) cc_final: 0.7811 (m-10) REVERT: A 521 ARG cc_start: 0.8858 (mtp180) cc_final: 0.8641 (mtp180) REVERT: B 40 GLU cc_start: 0.8143 (tp30) cc_final: 0.7720 (tp30) REVERT: B 93 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 98 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8556 (mp0) REVERT: B 474 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: B 480 MET cc_start: 0.8793 (mmm) cc_final: 0.8578 (mmm) outliers start: 31 outliers final: 20 residues processed: 85 average time/residue: 0.2210 time to fit residues: 26.7386 Evaluate side-chains 78 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP 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 98 GLU Chi-restraints excluded: chain B residue 115 LEU 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 474 GLU Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 0.0020 chunk 97 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 51 optimal weight: 0.0050 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.084238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.067466 restraints weight = 24413.091| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.95 r_work: 0.3091 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8317 Z= 0.105 Angle : 0.534 7.825 11309 Z= 0.268 Chirality : 0.041 0.162 1269 Planarity : 0.004 0.035 1479 Dihedral : 6.052 57.451 1162 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.95 % Allowed : 25.06 % 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: 0.75 (0.26), residues: 1026 helix: 1.95 (0.25), residues: 404 sheet: 0.02 (0.38), residues: 181 loop : -0.65 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.007 0.001 PHE A 102 TYR 0.014 0.001 TYR A 259 ARG 0.004 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 445) hydrogen bonds : angle 4.41595 ( 1260) SS BOND : bond 0.00265 ( 2) SS BOND : angle 1.33291 ( 4) covalent geometry : bond 0.00236 ( 8313) covalent geometry : angle 0.53397 (11305) Misc. bond : bond 0.00065 ( 2) *********************** 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 83 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: A 61 LEU cc_start: 0.8625 (mm) cc_final: 0.8412 (mp) REVERT: A 116 GLU cc_start: 0.8367 (pm20) cc_final: 0.7846 (pm20) REVERT: A 139 MET cc_start: 0.9445 (tmm) cc_final: 0.9181 (tmm) REVERT: A 316 GLU cc_start: 0.9132 (tp30) cc_final: 0.8905 (tp30) REVERT: A 328 ILE cc_start: 0.9558 (OUTLIER) cc_final: 0.9294 (mt) REVERT: A 337 MET cc_start: 0.9092 (ttp) cc_final: 0.8282 (ptm) REVERT: A 451 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7398 (t70) REVERT: A 476 TRP cc_start: 0.8295 (OUTLIER) cc_final: 0.7892 (t60) REVERT: A 521 ARG cc_start: 0.8839 (mtp180) cc_final: 0.8420 (mtp85) REVERT: B 22 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8064 (tp40) REVERT: B 40 GLU cc_start: 0.8075 (tp30) cc_final: 0.7615 (tp30) REVERT: B 93 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8004 (mp) REVERT: B 98 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: B 191 MET cc_start: 0.8653 (tpp) cc_final: 0.8015 (tpp) REVERT: B 458 LEU cc_start: 0.9253 (tp) cc_final: 0.8901 (mm) REVERT: B 474 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8472 (pm20) outliers start: 26 outliers final: 16 residues processed: 82 average time/residue: 0.1987 time to fit residues: 23.2521 Evaluate side-chains 76 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN 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 308 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 22 GLN 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 98 GLU 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 474 GLU 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 68 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.080011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.061032 restraints weight = 24072.717| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.10 r_work: 0.3032 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8317 Z= 0.121 Angle : 0.559 11.500 11309 Z= 0.278 Chirality : 0.041 0.157 1269 Planarity : 0.004 0.055 1479 Dihedral : 6.050 57.628 1162 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.72 % Allowed : 26.19 % Favored : 71.09 % 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: 0.79 (0.26), residues: 1026 helix: 1.96 (0.25), residues: 410 sheet: 0.04 (0.38), residues: 181 loop : -0.64 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.006 0.001 HIS B 144 PHE 0.007 0.001 PHE B 102 TYR 0.014 0.001 TYR A 259 ARG 0.014 0.000 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 445) hydrogen bonds : angle 4.42017 ( 1260) SS BOND : bond 0.00280 ( 2) SS BOND : angle 1.28056 ( 4) covalent geometry : bond 0.00275 ( 8313) covalent geometry : angle 0.55901 (11305) Misc. bond : bond 0.00070 ( 2) ********************** 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 77 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.927 Fit side-chains REVERT: A 45 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: A 61 LEU cc_start: 0.8740 (mm) cc_final: 0.8534 (mp) REVERT: A 116 GLU cc_start: 0.8472 (pm20) cc_final: 0.7990 (pm20) REVERT: A 139 MET cc_start: 0.9389 (tmm) cc_final: 0.9108 (tmm) REVERT: A 316 GLU cc_start: 0.9102 (tp30) cc_final: 0.8875 (tp30) REVERT: A 328 ILE cc_start: 0.9596 (OUTLIER) cc_final: 0.9331 (mt) REVERT: A 337 MET cc_start: 0.9031 (ttp) cc_final: 0.8240 (ptm) REVERT: A 451 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7471 (t70) REVERT: A 476 TRP cc_start: 0.8302 (OUTLIER) cc_final: 0.7936 (t60) REVERT: A 521 ARG cc_start: 0.8816 (mtp180) cc_final: 0.8468 (mtp85) REVERT: B 40 GLU cc_start: 0.8097 (tp30) cc_final: 0.7658 (tp30) REVERT: B 93 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 98 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: B 458 LEU cc_start: 0.9228 (tp) cc_final: 0.8893 (mm) REVERT: B 474 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8477 (pm20) REVERT: B 480 MET cc_start: 0.8592 (mmm) cc_final: 0.8089 (mmm) outliers start: 24 outliers final: 17 residues processed: 77 average time/residue: 0.1921 time to fit residues: 21.0397 Evaluate side-chains 75 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 GLN 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 308 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 476 TRP 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 98 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 GLU 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 5 optimal weight: 7.9990 chunk 64 optimal weight: 0.0170 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 chunk 91 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.3814 ------------------------------------------------------------------------------- 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** B 22 GLN ** B 241 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 = 0.3587 r_free = 0.3587 target = 0.080175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060976 restraints weight = 24359.158| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.17 r_work: 0.3054 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8317 Z= 0.103 Angle : 0.548 10.664 11309 Z= 0.273 Chirality : 0.041 0.158 1269 Planarity : 0.004 0.036 1479 Dihedral : 5.960 56.063 1162 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.49 % Allowed : 26.42 % Favored : 71.09 % 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: 1.98 (0.25), residues: 404 sheet: 0.13 (0.38), residues: 181 loop : -0.64 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 476 HIS 0.005 0.001 HIS B 144 PHE 0.007 0.001 PHE A 102 TYR 0.014 0.001 TYR A 259 ARG 0.007 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 445) hydrogen bonds : angle 4.39852 ( 1260) SS BOND : bond 0.00201 ( 2) SS BOND : angle 1.14909 ( 4) covalent geometry : bond 0.00231 ( 8313) covalent geometry : angle 0.54815 (11305) Misc. bond : bond 0.00058 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4393.34 seconds wall clock time: 77 minutes 47.16 seconds (4667.16 seconds total)