Starting phenix.real_space_refine on Fri Aug 22 21:21:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1x_38849/08_2025/8y1x_38849.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1x_38849/08_2025/8y1x_38849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y1x_38849/08_2025/8y1x_38849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1x_38849/08_2025/8y1x_38849.map" model { file = "/net/cci-nas-00/data/ceres_data/8y1x_38849/08_2025/8y1x_38849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1x_38849/08_2025/8y1x_38849.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 sd= 0.037 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 28 5.16 5 C 5294 2.51 5 N 1284 2.21 5 O 1468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8074 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4028 Classifications: {'peptide': 543} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 524} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: B Time building chain proxies: 2.66, per 1000 atoms: 0.33 Number of scatterers: 8074 At special positions: 0 Unit cell: (108.979, 81.1008, 109.824, 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 28 16.00 O 1468 8.00 N 1284 7.00 C 5294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 420.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 69.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 4.142A pdb=" N GLY A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 20 through 29 removed outlier: 4.098A pdb=" N TYR A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 58 through 88 removed outlier: 3.796A pdb=" N GLY A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Proline residue: A 79 - end of helix removed outlier: 4.199A pdb=" N ILE A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 115 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 132 through 145 removed outlier: 4.365A pdb=" N GLY A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 180 removed outlier: 3.748A pdb=" N ILE A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Proline residue: A 160 - end of helix removed outlier: 3.903A pdb=" N VAL A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.559A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.712A pdb=" N SER A 329 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.779A pdb=" N VAL A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 412 removed outlier: 3.616A pdb=" N SER A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 442 removed outlier: 3.717A pdb=" N LEU A 423 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 458 through 478 Proline residue: A 468 - end of helix Processing helix chain 'A' and resid 483 through 495 removed outlier: 3.735A pdb=" N ILE A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.616A pdb=" N GLY A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 543 removed outlier: 3.672A pdb=" N ALA A 518 " --> pdb=" O PRO A 514 " (cutoff:3.500A) Proline residue: A 522 - end of helix removed outlier: 4.217A pdb=" N ALA A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Proline residue: A 536 - end of helix Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 20 through 29 removed outlier: 4.097A pdb=" N TYR B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 58 through 88 removed outlier: 3.795A pdb=" N GLY B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Proline residue: B 79 - end of helix removed outlier: 4.199A pdb=" N ILE B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 115 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.365A pdb=" N GLY B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 180 removed outlier: 3.748A pdb=" N ILE B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) Proline residue: B 160 - end of helix removed outlier: 3.903A pdb=" N VAL B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 171 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 189 through 201 removed outlier: 3.560A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 266 through 277 Processing helix chain 'B' and resid 302 through 312 Processing helix chain 'B' and resid 324 through 329 removed outlier: 3.712A pdb=" N SER B 329 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 364 through 381 removed outlier: 3.779A pdb=" N VAL B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 412 removed outlier: 3.615A pdb=" N SER B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 442 removed outlier: 3.718A pdb=" N LEU B 423 " --> pdb=" O PRO B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 458 through 478 Proline residue: B 468 - end of helix Processing helix chain 'B' and resid 483 through 495 removed outlier: 3.736A pdb=" N ILE B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 488 " --> pdb=" O PRO B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 509 removed outlier: 3.616A pdb=" N GLY B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 543 removed outlier: 3.672A pdb=" N ALA B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Proline residue: B 522 - end of helix removed outlier: 4.217A pdb=" N ALA B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B 526 " --> pdb=" O PRO B 522 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Proline residue: B 536 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.687A pdb=" N ILE A 31 " --> pdb=" O PHE A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 214 removed outlier: 3.656A pdb=" N SER A 212 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 265 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA4, first strand: chain 'A' and resid 292 through 294 removed outlier: 3.637A pdb=" N VAL A 340 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 314 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 385 Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.687A pdb=" N ILE B 31 " --> pdb=" O PHE B 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 212 through 214 removed outlier: 3.656A pdb=" N SER B 212 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 265 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AA9, first strand: chain 'B' and resid 292 through 294 removed outlier: 3.637A pdb=" N VAL B 340 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 314 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 382 through 385 522 hydrogen bonds defined for protein. 1512 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: 1.22 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2508 1.34 - 1.46: 1217 1.46 - 1.57: 4437 1.57 - 1.69: 0 1.69 - 1.80: 56 Bond restraints: 8218 Sorted by residual: bond pdb=" CA SER B 513 " pdb=" CB SER B 513 " ideal model delta sigma weight residual 1.533 1.493 0.040 1.39e-02 5.18e+03 8.34e+00 bond pdb=" CA SER A 513 " pdb=" CB SER A 513 " ideal model delta sigma weight residual 1.533 1.493 0.040 1.39e-02 5.18e+03 8.24e+00 bond pdb=" N PHE B 515 " pdb=" CA PHE B 515 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.27e-02 6.20e+03 5.44e+00 bond pdb=" N SER A 513 " pdb=" CA SER A 513 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.04e-02 9.25e+03 5.26e+00 bond pdb=" N PHE A 515 " pdb=" CA PHE A 515 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.27e-02 6.20e+03 5.25e+00 ... (remaining 8213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 11002 2.14 - 4.29: 128 4.29 - 6.43: 26 6.43 - 8.57: 4 8.57 - 10.71: 2 Bond angle restraints: 11162 Sorted by residual: angle pdb=" N PHE B 515 " pdb=" CA PHE B 515 " pdb=" C PHE B 515 " ideal model delta sigma weight residual 112.04 107.05 4.99 1.44e+00 4.82e-01 1.20e+01 angle pdb=" N PHE A 515 " pdb=" CA PHE A 515 " pdb=" C PHE A 515 " ideal model delta sigma weight residual 112.04 107.08 4.96 1.44e+00 4.82e-01 1.19e+01 angle pdb=" N GLY A 78 " pdb=" CA GLY A 78 " pdb=" C GLY A 78 " ideal model delta sigma weight residual 112.34 118.62 -6.28 2.04e+00 2.40e-01 9.49e+00 angle pdb=" N GLY B 78 " pdb=" CA GLY B 78 " pdb=" C GLY B 78 " ideal model delta sigma weight residual 112.34 118.61 -6.27 2.04e+00 2.40e-01 9.45e+00 angle pdb=" CA LEU A 280 " pdb=" CB LEU A 280 " pdb=" CG LEU A 280 " ideal model delta sigma weight residual 116.30 127.01 -10.71 3.50e+00 8.16e-02 9.37e+00 ... (remaining 11157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.81: 4003 12.81 - 25.62: 499 25.62 - 38.43: 240 38.43 - 51.24: 80 51.24 - 64.05: 22 Dihedral angle restraints: 4844 sinusoidal: 1764 harmonic: 3080 Sorted by residual: dihedral pdb=" CA LEU B 129 " pdb=" C LEU B 129 " pdb=" N THR B 130 " pdb=" CA THR B 130 " ideal model delta harmonic sigma weight residual -180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LEU A 129 " pdb=" C LEU A 129 " pdb=" N THR A 130 " pdb=" CA THR A 130 " ideal model delta harmonic sigma weight residual -180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA THR B 217 " pdb=" C THR B 217 " pdb=" N ILE B 218 " pdb=" CA ILE B 218 " ideal model delta harmonic sigma weight residual 180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+00 ... (remaining 4841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 929 0.038 - 0.077: 312 0.077 - 0.115: 114 0.115 - 0.153: 23 0.153 - 0.191: 8 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CG LEU B 280 " pdb=" CB LEU B 280 " pdb=" CD1 LEU B 280 " pdb=" CD2 LEU B 280 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CG LEU A 280 " pdb=" CB LEU A 280 " pdb=" CD1 LEU A 280 " pdb=" CD2 LEU A 280 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CB THR A 153 " pdb=" CA THR A 153 " pdb=" OG1 THR A 153 " pdb=" CG2 THR A 153 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.92e-01 ... (remaining 1383 not shown) Planarity restraints: 1382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 455 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C ILE A 455 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE A 455 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 456 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 455 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C ILE B 455 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE B 455 " 0.013 2.00e-02 2.50e+03 pdb=" N SER B 456 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 427 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C GLN B 427 " -0.020 2.00e-02 2.50e+03 pdb=" O GLN B 427 " 0.007 2.00e-02 2.50e+03 pdb=" N SER B 428 " 0.007 2.00e-02 2.50e+03 ... (remaining 1379 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2228 2.81 - 3.33: 8094 3.33 - 3.86: 12905 3.86 - 4.38: 13929 4.38 - 4.90: 25122 Nonbonded interactions: 62278 Sorted by model distance: nonbonded pdb=" OD1 ASP B 268 " pdb=" NH1 ARG B 272 " model vdw 2.289 3.120 nonbonded pdb=" OD1 ASP A 268 " pdb=" NH1 ARG A 272 " model vdw 2.289 3.120 nonbonded pdb=" OG1 THR B 217 " pdb=" O GLY B 258 " model vdw 2.322 3.040 nonbonded pdb=" OG1 THR A 217 " pdb=" O GLY A 258 " model vdw 2.323 3.040 nonbonded pdb=" OG SER A 84 " pdb=" O ALA A 518 " model vdw 2.361 3.040 ... (remaining 62273 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.460 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 0.040 8218 Z= 0.170 Angle : 0.650 10.714 11162 Z= 0.347 Chirality : 0.046 0.191 1386 Planarity : 0.004 0.027 1382 Dihedral : 15.439 64.045 2876 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.46 % Allowed : 25.75 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1082 helix: 1.24 (0.20), residues: 720 sheet: -2.40 (0.55), residues: 62 loop : -1.43 (0.30), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 409 TYR 0.011 0.001 TYR A 289 PHE 0.014 0.001 PHE B 169 TRP 0.007 0.002 TRP B 367 HIS 0.001 0.000 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8218) covalent geometry : angle 0.64970 (11162) hydrogen bonds : bond 0.10451 ( 522) hydrogen bonds : angle 5.06647 ( 1512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 VAL cc_start: 0.9588 (t) cc_final: 0.9110 (p) REVERT: B 216 TYR cc_start: 0.7502 (m-80) cc_final: 0.6761 (m-80) REVERT: B 251 MET cc_start: 0.7954 (mmt) cc_final: 0.7681 (mmp) REVERT: B 315 VAL cc_start: 0.8761 (m) cc_final: 0.8499 (p) REVERT: B 323 MET cc_start: 0.7558 (ppp) cc_final: 0.7234 (ppp) outliers start: 4 outliers final: 2 residues processed: 215 average time/residue: 0.0708 time to fit residues: 21.6761 Evaluate side-chains 111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain B residue 55 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 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 412 HIS A 427 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.041510 restraints weight = 41184.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.042948 restraints weight = 23040.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.043904 restraints weight = 15524.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.044729 restraints weight = 11833.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.045356 restraints weight = 9393.243| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8218 Z= 0.128 Angle : 0.653 10.286 11162 Z= 0.323 Chirality : 0.044 0.219 1386 Planarity : 0.004 0.035 1382 Dihedral : 4.503 37.197 1136 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.76 % Allowed : 28.31 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.26), residues: 1082 helix: 1.35 (0.20), residues: 738 sheet: -2.35 (0.57), residues: 62 loop : -1.49 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 272 TYR 0.018 0.001 TYR A 163 PHE 0.017 0.001 PHE A 426 TRP 0.004 0.001 TRP A 367 HIS 0.004 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8218) covalent geometry : angle 0.65347 (11162) hydrogen bonds : bond 0.04200 ( 522) hydrogen bonds : angle 4.55520 ( 1512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9526 (tpp) cc_final: 0.9171 (mpp) REVERT: A 140 GLU cc_start: 0.9138 (tp30) cc_final: 0.8862 (tp30) REVERT: A 182 MET cc_start: 0.9425 (tpp) cc_final: 0.9151 (tmm) REVERT: A 269 GLU cc_start: 0.9527 (mp0) cc_final: 0.9290 (mp0) REVERT: A 323 MET cc_start: 0.8310 (ppp) cc_final: 0.6865 (ppp) REVERT: A 431 LEU cc_start: 0.9383 (tp) cc_final: 0.8973 (mt) REVERT: A 480 MET cc_start: 0.9233 (ttm) cc_final: 0.8674 (ptm) REVERT: A 541 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8951 (mm) REVERT: B 131 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8877 (tm-30) REVERT: B 213 THR cc_start: 0.9262 (p) cc_final: 0.9060 (t) REVERT: B 216 TYR cc_start: 0.9260 (m-80) cc_final: 0.9015 (m-80) REVERT: B 241 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8950 (p) REVERT: B 323 MET cc_start: 0.8597 (ppp) cc_final: 0.7885 (ppp) REVERT: B 339 LEU cc_start: 0.9782 (mt) cc_final: 0.9263 (pt) REVERT: B 531 LEU cc_start: 0.9536 (tp) cc_final: 0.9274 (tp) REVERT: B 541 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9041 (mm) outliers start: 41 outliers final: 17 residues processed: 151 average time/residue: 0.0610 time to fit residues: 13.9744 Evaluate side-chains 123 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 13 optimal weight: 0.0470 chunk 106 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 6 ASN B 2 ASN B 412 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.040395 restraints weight = 40958.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.041829 restraints weight = 22951.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.042855 restraints weight = 15367.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.043502 restraints weight = 11563.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.044101 restraints weight = 9460.211| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8218 Z= 0.133 Angle : 0.651 13.230 11162 Z= 0.312 Chirality : 0.043 0.157 1386 Planarity : 0.003 0.027 1382 Dihedral : 4.332 41.082 1136 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.99 % Allowed : 27.61 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.26), residues: 1082 helix: 1.63 (0.20), residues: 734 sheet: -2.06 (0.60), residues: 62 loop : -1.50 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.018 0.001 TYR A 163 PHE 0.022 0.002 PHE B 236 TRP 0.002 0.001 TRP B 367 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8218) covalent geometry : angle 0.65139 (11162) hydrogen bonds : bond 0.04131 ( 522) hydrogen bonds : angle 4.36696 ( 1512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.9245 (OUTLIER) cc_final: 0.8589 (t0) REVERT: A 6 ASN cc_start: 0.9798 (OUTLIER) cc_final: 0.9513 (m-40) REVERT: A 70 MET cc_start: 0.9541 (tpp) cc_final: 0.9218 (mpp) REVERT: A 140 GLU cc_start: 0.9135 (tp30) cc_final: 0.8804 (tp30) REVERT: A 182 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.9170 (tmm) REVERT: A 186 MET cc_start: 0.9158 (mmm) cc_final: 0.8730 (mmm) REVERT: A 314 LEU cc_start: 0.9577 (tp) cc_final: 0.9371 (tt) REVERT: A 323 MET cc_start: 0.8577 (ppp) cc_final: 0.8364 (ppp) REVERT: A 431 LEU cc_start: 0.9448 (tp) cc_final: 0.9091 (mt) REVERT: A 541 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8984 (mm) REVERT: B 131 GLN cc_start: 0.9261 (tm-30) cc_final: 0.9022 (tm-30) REVERT: B 140 GLU cc_start: 0.9160 (tp30) cc_final: 0.8917 (tp30) REVERT: B 241 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9224 (p) REVERT: B 323 MET cc_start: 0.8722 (ppp) cc_final: 0.7647 (ppp) REVERT: B 339 LEU cc_start: 0.9766 (mt) cc_final: 0.9222 (pt) REVERT: B 531 LEU cc_start: 0.9512 (tp) cc_final: 0.9250 (tp) REVERT: B 541 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9083 (mm) outliers start: 43 outliers final: 17 residues processed: 142 average time/residue: 0.0595 time to fit residues: 13.0666 Evaluate side-chains 111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 6 ASN Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 45 optimal weight: 0.0980 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.050483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.036111 restraints weight = 44302.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.037406 restraints weight = 24778.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.038365 restraints weight = 16681.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.038986 restraints weight = 12668.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.039432 restraints weight = 10396.280| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8218 Z= 0.244 Angle : 0.719 10.719 11162 Z= 0.360 Chirality : 0.043 0.149 1386 Planarity : 0.004 0.035 1382 Dihedral : 4.623 48.397 1136 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.15 % Allowed : 27.03 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.26), residues: 1082 helix: 1.67 (0.20), residues: 734 sheet: -1.98 (0.62), residues: 62 loop : -1.58 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 355 TYR 0.011 0.001 TYR B 167 PHE 0.018 0.002 PHE B 473 TRP 0.004 0.001 TRP B 367 HIS 0.003 0.001 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 8218) covalent geometry : angle 0.71893 (11162) hydrogen bonds : bond 0.04792 ( 522) hydrogen bonds : angle 4.74506 ( 1512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 89 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9601 (tpp) cc_final: 0.9153 (mpp) REVERT: A 80 SER cc_start: 0.9735 (m) cc_final: 0.9353 (t) REVERT: A 140 GLU cc_start: 0.9166 (tp30) cc_final: 0.8814 (tp30) REVERT: A 182 MET cc_start: 0.9492 (OUTLIER) cc_final: 0.9256 (tmm) REVERT: A 218 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8321 (mm) REVERT: A 323 MET cc_start: 0.8888 (ppp) cc_final: 0.8561 (ppp) REVERT: A 437 THR cc_start: 0.9700 (OUTLIER) cc_final: 0.9345 (p) REVERT: A 541 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9044 (mm) REVERT: B 131 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8855 (tm-30) REVERT: B 140 GLU cc_start: 0.9168 (tp30) cc_final: 0.8908 (tp30) REVERT: B 182 MET cc_start: 0.9522 (tmm) cc_final: 0.9197 (tmm) REVERT: B 218 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8141 (mm) REVERT: B 323 MET cc_start: 0.8926 (ppp) cc_final: 0.8044 (ppp) REVERT: B 531 LEU cc_start: 0.9561 (tp) cc_final: 0.9356 (tp) REVERT: B 541 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9084 (mm) outliers start: 53 outliers final: 28 residues processed: 138 average time/residue: 0.0585 time to fit residues: 12.7590 Evaluate side-chains 117 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 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 = 0.3024 r_free = 0.3024 target = 0.052039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.037129 restraints weight = 42830.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.038424 restraints weight = 24300.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.039338 restraints weight = 16565.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.039916 restraints weight = 12608.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.040457 restraints weight = 10472.138| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8218 Z= 0.186 Angle : 0.687 12.118 11162 Z= 0.332 Chirality : 0.043 0.162 1386 Planarity : 0.003 0.033 1382 Dihedral : 4.585 54.232 1136 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.87 % Allowed : 28.54 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.26), residues: 1082 helix: 1.72 (0.20), residues: 734 sheet: -1.90 (0.62), residues: 62 loop : -1.71 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 409 TYR 0.009 0.001 TYR A 289 PHE 0.016 0.002 PHE A 300 TRP 0.003 0.001 TRP B 367 HIS 0.003 0.001 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8218) covalent geometry : angle 0.68696 (11162) hydrogen bonds : bond 0.04352 ( 522) hydrogen bonds : angle 4.51697 ( 1512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9618 (tpp) cc_final: 0.9120 (mpp) REVERT: A 80 SER cc_start: 0.9697 (m) cc_final: 0.9283 (t) REVERT: A 140 GLU cc_start: 0.9159 (tp30) cc_final: 0.8788 (tp30) REVERT: A 182 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.9220 (tmm) REVERT: A 218 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 323 MET cc_start: 0.9008 (ppp) cc_final: 0.8638 (ppp) REVERT: A 415 MET cc_start: 0.8831 (mpp) cc_final: 0.8234 (mpp) REVERT: A 431 LEU cc_start: 0.9516 (tp) cc_final: 0.9251 (mt) REVERT: A 437 THR cc_start: 0.9670 (OUTLIER) cc_final: 0.9314 (p) REVERT: A 541 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9008 (mm) REVERT: B 48 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9486 (mm) REVERT: B 80 SER cc_start: 0.9637 (m) cc_final: 0.9182 (t) REVERT: B 140 GLU cc_start: 0.9151 (tp30) cc_final: 0.8876 (tp30) REVERT: B 182 MET cc_start: 0.9560 (tmm) cc_final: 0.9199 (tmm) REVERT: B 218 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8137 (mm) REVERT: B 269 GLU cc_start: 0.9500 (mp0) cc_final: 0.9084 (pm20) REVERT: B 323 MET cc_start: 0.9006 (ppp) cc_final: 0.8252 (ppp) REVERT: B 339 LEU cc_start: 0.9741 (mt) cc_final: 0.9237 (pt) REVERT: B 431 LEU cc_start: 0.9522 (tp) cc_final: 0.9194 (mt) REVERT: B 541 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9065 (mm) outliers start: 42 outliers final: 25 residues processed: 130 average time/residue: 0.0572 time to fit residues: 11.6858 Evaluate side-chains 115 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 17 optimal weight: 0.0470 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 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 = 0.3027 r_free = 0.3027 target = 0.051640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.036919 restraints weight = 42831.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.038209 restraints weight = 24115.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.039160 restraints weight = 16451.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.039760 restraints weight = 12487.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.040341 restraints weight = 10261.554| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8218 Z= 0.171 Angle : 0.683 10.868 11162 Z= 0.329 Chirality : 0.043 0.157 1386 Planarity : 0.003 0.032 1382 Dihedral : 4.656 58.284 1136 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.76 % Allowed : 29.81 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.26), residues: 1082 helix: 1.81 (0.20), residues: 734 sheet: -1.91 (0.61), residues: 62 loop : -1.73 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 409 TYR 0.009 0.001 TYR A 163 PHE 0.015 0.001 PHE A 300 TRP 0.002 0.001 TRP B 367 HIS 0.003 0.001 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8218) covalent geometry : angle 0.68259 (11162) hydrogen bonds : bond 0.04221 ( 522) hydrogen bonds : angle 4.49455 ( 1512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9630 (tpp) cc_final: 0.9170 (mpp) REVERT: A 80 SER cc_start: 0.9688 (m) cc_final: 0.9269 (t) REVERT: A 140 GLU cc_start: 0.9149 (tp30) cc_final: 0.8767 (tp30) REVERT: A 182 MET cc_start: 0.9475 (OUTLIER) cc_final: 0.9229 (tmm) REVERT: A 203 MET cc_start: 0.9544 (mmm) cc_final: 0.9326 (mmm) REVERT: A 218 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8319 (mm) REVERT: A 269 GLU cc_start: 0.9530 (mp0) cc_final: 0.9097 (pm20) REVERT: A 323 MET cc_start: 0.9061 (ppp) cc_final: 0.8680 (ppp) REVERT: A 415 MET cc_start: 0.8836 (mpp) cc_final: 0.8224 (mpp) REVERT: A 431 LEU cc_start: 0.9507 (tp) cc_final: 0.9251 (mt) REVERT: A 437 THR cc_start: 0.9670 (OUTLIER) cc_final: 0.9316 (p) REVERT: A 480 MET cc_start: 0.9135 (ptm) cc_final: 0.8476 (ppp) REVERT: A 541 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9063 (mm) REVERT: B 48 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9482 (mm) REVERT: B 80 SER cc_start: 0.9643 (m) cc_final: 0.9196 (t) REVERT: B 113 MET cc_start: 0.9250 (tmm) cc_final: 0.9015 (ppp) REVERT: B 140 GLU cc_start: 0.9158 (tp30) cc_final: 0.8881 (tp30) REVERT: B 182 MET cc_start: 0.9546 (tmm) cc_final: 0.9130 (tmm) REVERT: B 218 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8113 (mm) REVERT: B 269 GLU cc_start: 0.9482 (mp0) cc_final: 0.9042 (pm20) REVERT: B 323 MET cc_start: 0.9041 (ppp) cc_final: 0.8356 (ppp) REVERT: B 339 LEU cc_start: 0.9737 (mt) cc_final: 0.9231 (pt) REVERT: B 424 GLU cc_start: 0.8831 (pp20) cc_final: 0.8437 (pp20) REVERT: B 541 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9056 (mm) outliers start: 41 outliers final: 29 residues processed: 129 average time/residue: 0.0556 time to fit residues: 11.3375 Evaluate side-chains 117 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.051958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.037164 restraints weight = 42660.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.038439 restraints weight = 24337.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.039350 restraints weight = 16754.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.040020 restraints weight = 12796.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.040467 restraints weight = 10516.550| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8218 Z= 0.158 Angle : 0.691 11.324 11162 Z= 0.327 Chirality : 0.043 0.153 1386 Planarity : 0.003 0.031 1382 Dihedral : 4.702 58.269 1136 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.18 % Allowed : 30.86 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.26), residues: 1082 helix: 1.85 (0.20), residues: 734 sheet: -2.03 (0.58), residues: 62 loop : -1.67 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.012 0.001 TYR B 216 PHE 0.015 0.001 PHE A 300 TRP 0.002 0.001 TRP B 367 HIS 0.003 0.001 HIS A 469 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8218) covalent geometry : angle 0.69144 (11162) hydrogen bonds : bond 0.04092 ( 522) hydrogen bonds : angle 4.38971 ( 1512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9618 (tpp) cc_final: 0.9143 (mpp) REVERT: A 80 SER cc_start: 0.9670 (m) cc_final: 0.9242 (t) REVERT: A 113 MET cc_start: 0.9289 (tmm) cc_final: 0.9012 (ppp) REVERT: A 140 GLU cc_start: 0.9174 (tp30) cc_final: 0.8800 (tp30) REVERT: A 182 MET cc_start: 0.9508 (OUTLIER) cc_final: 0.9236 (tmm) REVERT: A 203 MET cc_start: 0.9567 (mmm) cc_final: 0.9316 (mmm) REVERT: A 218 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8309 (mm) REVERT: A 269 GLU cc_start: 0.9544 (mp0) cc_final: 0.9085 (pm20) REVERT: A 323 MET cc_start: 0.9119 (ppp) cc_final: 0.8802 (ppp) REVERT: A 396 THR cc_start: 0.9556 (OUTLIER) cc_final: 0.9280 (p) REVERT: A 415 MET cc_start: 0.8858 (mpp) cc_final: 0.8162 (mpp) REVERT: A 431 LEU cc_start: 0.9500 (tp) cc_final: 0.9256 (mt) REVERT: B 48 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9479 (mm) REVERT: B 70 MET cc_start: 0.9625 (mmm) cc_final: 0.9065 (mpp) REVERT: B 80 SER cc_start: 0.9633 (m) cc_final: 0.9190 (t) REVERT: B 140 GLU cc_start: 0.9140 (tp30) cc_final: 0.8859 (tp30) REVERT: B 182 MET cc_start: 0.9569 (tmm) cc_final: 0.9140 (tmm) REVERT: B 203 MET cc_start: 0.9388 (mmp) cc_final: 0.9040 (mmp) REVERT: B 218 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8218 (mm) REVERT: B 323 MET cc_start: 0.9026 (ppp) cc_final: 0.8444 (ppp) REVERT: B 339 LEU cc_start: 0.9719 (mt) cc_final: 0.9201 (pt) REVERT: B 431 LEU cc_start: 0.9503 (tp) cc_final: 0.9210 (mt) REVERT: B 541 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9036 (mm) outliers start: 36 outliers final: 26 residues processed: 125 average time/residue: 0.0544 time to fit residues: 10.6213 Evaluate side-chains 119 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 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 = 0.3035 r_free = 0.3035 target = 0.051675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.036837 restraints weight = 42803.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.038125 restraints weight = 24433.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.039039 restraints weight = 16764.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.039637 restraints weight = 12798.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.040162 restraints weight = 10579.075| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8218 Z= 0.170 Angle : 0.716 11.698 11162 Z= 0.340 Chirality : 0.043 0.158 1386 Planarity : 0.003 0.030 1382 Dihedral : 4.706 55.849 1136 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.29 % Allowed : 31.55 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.26), residues: 1082 helix: 1.81 (0.20), residues: 736 sheet: -1.98 (0.59), residues: 62 loop : -1.63 (0.32), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.009 0.001 TYR B 216 PHE 0.015 0.001 PHE A 300 TRP 0.002 0.001 TRP B 367 HIS 0.002 0.001 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8218) covalent geometry : angle 0.71619 (11162) hydrogen bonds : bond 0.04123 ( 522) hydrogen bonds : angle 4.43737 ( 1512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.315 Fit side-chains REVERT: A 70 MET cc_start: 0.9610 (tpp) cc_final: 0.9133 (mpp) REVERT: A 80 SER cc_start: 0.9674 (m) cc_final: 0.9251 (t) REVERT: A 113 MET cc_start: 0.9324 (tmm) cc_final: 0.9096 (ppp) REVERT: A 140 GLU cc_start: 0.9167 (tp30) cc_final: 0.8793 (tp30) REVERT: A 182 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.9219 (tmm) REVERT: A 203 MET cc_start: 0.9584 (mmm) cc_final: 0.9329 (mmm) REVERT: A 218 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8352 (mm) REVERT: A 323 MET cc_start: 0.9131 (ppp) cc_final: 0.8814 (ppp) REVERT: A 396 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9302 (p) REVERT: A 415 MET cc_start: 0.8866 (mpp) cc_final: 0.8177 (mpp) REVERT: A 431 LEU cc_start: 0.9498 (tp) cc_final: 0.9241 (mt) REVERT: A 437 THR cc_start: 0.9667 (OUTLIER) cc_final: 0.9317 (p) REVERT: B 48 LEU cc_start: 0.9737 (OUTLIER) cc_final: 0.9489 (mm) REVERT: B 55 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8532 (p90) REVERT: B 70 MET cc_start: 0.9625 (mmm) cc_final: 0.9082 (mpp) REVERT: B 80 SER cc_start: 0.9630 (m) cc_final: 0.9188 (t) REVERT: B 113 MET cc_start: 0.9333 (tmm) cc_final: 0.9075 (ppp) REVERT: B 140 GLU cc_start: 0.9137 (tp30) cc_final: 0.8854 (tp30) REVERT: B 182 MET cc_start: 0.9567 (tmm) cc_final: 0.9120 (tmm) REVERT: B 218 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8309 (mm) REVERT: B 269 GLU cc_start: 0.9505 (mp0) cc_final: 0.9086 (pm20) REVERT: B 323 MET cc_start: 0.9062 (ppp) cc_final: 0.8580 (ppp) REVERT: B 431 LEU cc_start: 0.9494 (tp) cc_final: 0.9183 (mt) REVERT: B 541 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9048 (mm) outliers start: 37 outliers final: 27 residues processed: 124 average time/residue: 0.0582 time to fit residues: 11.1981 Evaluate side-chains 116 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 92 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 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 = 0.3035 r_free = 0.3035 target = 0.051628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.036846 restraints weight = 42353.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.038125 restraints weight = 24167.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.039068 restraints weight = 16577.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.039714 restraints weight = 12593.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.040202 restraints weight = 10354.575| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8218 Z= 0.158 Angle : 0.730 11.913 11162 Z= 0.346 Chirality : 0.043 0.147 1386 Planarity : 0.003 0.031 1382 Dihedral : 4.703 54.328 1136 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.29 % Allowed : 31.21 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.26), residues: 1082 helix: 1.85 (0.20), residues: 736 sheet: -1.86 (0.60), residues: 62 loop : -1.63 (0.32), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.009 0.001 TYR B 289 PHE 0.020 0.001 PHE B 277 TRP 0.002 0.001 TRP B 367 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8218) covalent geometry : angle 0.72970 (11162) hydrogen bonds : bond 0.04066 ( 522) hydrogen bonds : angle 4.38468 ( 1512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.196 Fit side-chains REVERT: A 70 MET cc_start: 0.9605 (tpp) cc_final: 0.9130 (mpp) REVERT: A 80 SER cc_start: 0.9666 (m) cc_final: 0.9233 (t) REVERT: A 140 GLU cc_start: 0.9148 (tp30) cc_final: 0.8755 (tp30) REVERT: A 182 MET cc_start: 0.9495 (OUTLIER) cc_final: 0.9193 (tmm) REVERT: A 203 MET cc_start: 0.9596 (mmm) cc_final: 0.9336 (mmm) REVERT: A 218 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8328 (mm) REVERT: A 269 GLU cc_start: 0.9537 (mp0) cc_final: 0.9041 (pm20) REVERT: A 323 MET cc_start: 0.9133 (ppp) cc_final: 0.8805 (ppp) REVERT: A 396 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9229 (p) REVERT: A 415 MET cc_start: 0.8870 (mpp) cc_final: 0.8218 (mpp) REVERT: A 431 LEU cc_start: 0.9516 (tp) cc_final: 0.9263 (mt) REVERT: A 437 THR cc_start: 0.9662 (OUTLIER) cc_final: 0.9310 (p) REVERT: B 48 LEU cc_start: 0.9737 (OUTLIER) cc_final: 0.9496 (mm) REVERT: B 55 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8578 (p90) REVERT: B 70 MET cc_start: 0.9616 (mmm) cc_final: 0.9067 (mpp) REVERT: B 80 SER cc_start: 0.9632 (m) cc_final: 0.9190 (t) REVERT: B 113 MET cc_start: 0.9327 (tmm) cc_final: 0.9090 (ppp) REVERT: B 140 GLU cc_start: 0.9127 (tp30) cc_final: 0.8838 (tp30) REVERT: B 182 MET cc_start: 0.9560 (tmm) cc_final: 0.9150 (tmm) REVERT: B 218 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8417 (mm) REVERT: B 251 MET cc_start: 0.9561 (mmp) cc_final: 0.9351 (mmt) REVERT: B 269 GLU cc_start: 0.9487 (mp0) cc_final: 0.9063 (pm20) REVERT: B 323 MET cc_start: 0.9087 (ppp) cc_final: 0.8620 (ppp) REVERT: B 431 LEU cc_start: 0.9514 (tp) cc_final: 0.9217 (mt) REVERT: B 541 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9033 (mm) outliers start: 37 outliers final: 27 residues processed: 118 average time/residue: 0.0478 time to fit residues: 9.0085 Evaluate side-chains 117 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 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 = 0.3062 r_free = 0.3062 target = 0.052614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.038076 restraints weight = 42319.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.039409 restraints weight = 23917.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.040395 restraints weight = 16312.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.041114 restraints weight = 12365.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.041608 restraints weight = 10017.399| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8218 Z= 0.132 Angle : 0.753 12.216 11162 Z= 0.348 Chirality : 0.043 0.155 1386 Planarity : 0.003 0.032 1382 Dihedral : 4.669 53.308 1136 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.48 % Allowed : 32.60 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.26), residues: 1082 helix: 1.90 (0.20), residues: 738 sheet: -1.80 (0.59), residues: 62 loop : -1.58 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.008 0.001 TYR A 163 PHE 0.026 0.001 PHE A 68 TRP 0.001 0.001 TRP B 367 HIS 0.003 0.000 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8218) covalent geometry : angle 0.75296 (11162) hydrogen bonds : bond 0.03765 ( 522) hydrogen bonds : angle 4.26900 ( 1512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9587 (tpp) cc_final: 0.9126 (mpp) REVERT: A 80 SER cc_start: 0.9653 (m) cc_final: 0.9220 (t) REVERT: A 140 GLU cc_start: 0.9127 (tp30) cc_final: 0.8729 (tp30) REVERT: A 182 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.9263 (tpp) REVERT: A 203 MET cc_start: 0.9593 (mmm) cc_final: 0.9331 (mmm) REVERT: A 218 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8320 (mm) REVERT: A 269 GLU cc_start: 0.9529 (mp0) cc_final: 0.9131 (pm20) REVERT: A 323 MET cc_start: 0.9101 (ppp) cc_final: 0.8749 (ppp) REVERT: A 415 MET cc_start: 0.8856 (mpp) cc_final: 0.8203 (mpp) REVERT: A 424 GLU cc_start: 0.8897 (pp20) cc_final: 0.8527 (pp20) REVERT: A 431 LEU cc_start: 0.9477 (tp) cc_final: 0.9259 (mt) REVERT: B 48 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9490 (mm) REVERT: B 55 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8688 (p90) REVERT: B 70 MET cc_start: 0.9591 (mmm) cc_final: 0.9034 (mpp) REVERT: B 80 SER cc_start: 0.9617 (m) cc_final: 0.9177 (t) REVERT: B 113 MET cc_start: 0.9316 (tmm) cc_final: 0.9077 (ppp) REVERT: B 140 GLU cc_start: 0.9102 (tp30) cc_final: 0.8807 (tp30) REVERT: B 182 MET cc_start: 0.9542 (tmm) cc_final: 0.9054 (tmm) REVERT: B 218 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8335 (mm) REVERT: B 269 GLU cc_start: 0.9490 (mp0) cc_final: 0.9061 (pm20) REVERT: B 323 MET cc_start: 0.9023 (ppp) cc_final: 0.8533 (ppp) REVERT: B 541 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8984 (mm) outliers start: 30 outliers final: 20 residues processed: 117 average time/residue: 0.0570 time to fit residues: 10.4351 Evaluate side-chains 111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.038936 restraints weight = 42182.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.040341 restraints weight = 23783.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.041361 restraints weight = 16248.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.042116 restraints weight = 12302.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.042629 restraints weight = 9946.312| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8218 Z= 0.120 Angle : 0.751 12.892 11162 Z= 0.342 Chirality : 0.043 0.173 1386 Planarity : 0.003 0.032 1382 Dihedral : 4.629 52.470 1136 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.90 % Allowed : 33.18 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.26), residues: 1082 helix: 1.97 (0.20), residues: 734 sheet: -1.81 (0.58), residues: 62 loop : -1.55 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.008 0.001 TYR B 289 PHE 0.019 0.001 PHE A 68 TRP 0.001 0.000 TRP B 367 HIS 0.003 0.000 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8218) covalent geometry : angle 0.75074 (11162) hydrogen bonds : bond 0.03483 ( 522) hydrogen bonds : angle 4.16931 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1198.34 seconds wall clock time: 21 minutes 26.22 seconds (1286.22 seconds total)