Starting phenix.real_space_refine on Mon Apr 28 20:36:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1x_38849/04_2025/8y1x_38849.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1x_38849/04_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_38849/04_2025/8y1x_38849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1x_38849/04_2025/8y1x_38849.map" model { file = "/net/cci-nas-00/data/ceres_data/8y1x_38849/04_2025/8y1x_38849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1x_38849/04_2025/8y1x_38849.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.52, per 1000 atoms: 0.93 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: 2.08 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.89 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: 2.41 Time building geometry restraints manager: 2.46 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.180 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (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 TRP 0.007 0.002 TRP B 367 HIS 0.001 0.000 HIS B 187 PHE 0.014 0.001 PHE B 169 TYR 0.011 0.001 TYR A 289 ARG 0.006 0.001 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.10451 ( 522) hydrogen bonds : angle 5.06647 ( 1512) covalent geometry : bond 0.00318 ( 8218) covalent geometry : angle 0.64970 (11162) *********************** 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 : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 VAL cc_start: 0.9588 (t) cc_final: 0.8955 (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: 0.1777 time to fit residues: 53.5507 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 : 0.900 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3082 r_free = 0.3082 target = 0.054841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.040342 restraints weight = 40676.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.041735 restraints weight = 23283.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.042644 restraints weight = 15758.237| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8218 Z= 0.133 Angle : 0.645 10.211 11162 Z= 0.322 Chirality : 0.044 0.201 1386 Planarity : 0.004 0.034 1382 Dihedral : 4.530 39.086 1136 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.10 % Allowed : 27.61 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1082 helix: 1.41 (0.20), residues: 738 sheet: -2.30 (0.58), residues: 62 loop : -1.48 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 367 HIS 0.004 0.001 HIS A 414 PHE 0.017 0.002 PHE A 236 TYR 0.018 0.001 TYR A 163 ARG 0.004 0.001 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 522) hydrogen bonds : angle 4.56932 ( 1512) covalent geometry : bond 0.00283 ( 8218) covalent geometry : angle 0.64474 (11162) *********************** 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: 44 poor density : 120 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.9187 (tp30) cc_final: 0.8918 (tp30) REVERT: A 182 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.9120 (tmm) REVERT: A 269 GLU cc_start: 0.9516 (mp0) cc_final: 0.9288 (mp0) REVERT: A 323 MET cc_start: 0.8454 (ppp) cc_final: 0.7125 (ppp) REVERT: A 380 ILE cc_start: 0.7711 (mm) cc_final: 0.7507 (mm) REVERT: A 431 LEU cc_start: 0.9408 (tp) cc_final: 0.8971 (mt) REVERT: A 480 MET cc_start: 0.9244 (ttm) cc_final: 0.8680 (ptm) REVERT: A 541 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8968 (mm) REVERT: B 131 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8824 (tm-30) REVERT: B 213 THR cc_start: 0.9244 (p) cc_final: 0.9019 (t) REVERT: B 216 TYR cc_start: 0.9297 (m-80) cc_final: 0.8939 (m-80) REVERT: B 241 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8948 (p) REVERT: B 269 GLU cc_start: 0.9442 (mp0) cc_final: 0.9238 (mp0) REVERT: B 323 MET cc_start: 0.8660 (ppp) cc_final: 0.7955 (ppp) REVERT: B 339 LEU cc_start: 0.9790 (mt) cc_final: 0.9238 (pt) REVERT: B 531 LEU cc_start: 0.9552 (tp) cc_final: 0.9307 (tp) outliers start: 44 outliers final: 18 residues processed: 151 average time/residue: 0.1486 time to fit residues: 33.3065 Evaluate side-chains 118 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 132 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 MET 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 400 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 539 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.053986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.039496 restraints weight = 41901.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.040909 restraints weight = 23284.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.041931 restraints weight = 15750.152| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8218 Z= 0.146 Angle : 0.653 13.418 11162 Z= 0.315 Chirality : 0.043 0.144 1386 Planarity : 0.003 0.031 1382 Dihedral : 4.340 43.002 1136 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.34 % Allowed : 27.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1082 helix: 1.64 (0.20), residues: 734 sheet: -2.08 (0.60), residues: 62 loop : -1.51 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 367 HIS 0.002 0.001 HIS B 469 PHE 0.015 0.002 PHE A 300 TYR 0.018 0.001 TYR A 163 ARG 0.003 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 522) hydrogen bonds : angle 4.38038 ( 1512) covalent geometry : bond 0.00319 ( 8218) covalent geometry : angle 0.65288 (11162) *********************** 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 144 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 98 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9571 (tpp) cc_final: 0.9201 (mpp) REVERT: A 140 GLU cc_start: 0.9142 (tp30) cc_final: 0.8815 (tp30) REVERT: A 182 MET cc_start: 0.9490 (tpp) cc_final: 0.9207 (tmm) REVERT: A 314 LEU cc_start: 0.9583 (tp) cc_final: 0.9380 (tt) REVERT: A 380 ILE cc_start: 0.7648 (mm) cc_final: 0.7427 (mm) REVERT: A 431 LEU cc_start: 0.9478 (tp) cc_final: 0.9076 (mt) REVERT: A 437 THR cc_start: 0.9615 (OUTLIER) cc_final: 0.9234 (p) REVERT: A 480 MET cc_start: 0.9302 (ttm) cc_final: 0.8799 (ptm) REVERT: A 541 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9006 (mm) REVERT: B 131 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8913 (tm-30) REVERT: B 140 GLU cc_start: 0.9152 (tp30) cc_final: 0.8922 (tp30) REVERT: B 218 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7779 (mm) REVERT: B 241 VAL cc_start: 0.9446 (OUTLIER) cc_final: 0.9212 (p) REVERT: B 323 MET cc_start: 0.8837 (ppp) cc_final: 0.7875 (ppp) REVERT: B 339 LEU cc_start: 0.9766 (mt) cc_final: 0.9217 (pt) outliers start: 46 outliers final: 22 residues processed: 139 average time/residue: 0.1432 time to fit residues: 30.2852 Evaluate side-chains 114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 285 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 VAL 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 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 241 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 539 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3040 r_free = 0.3040 target = 0.052058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.037371 restraints weight = 42824.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.038674 restraints weight = 24231.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.039644 restraints weight = 16627.897| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3859 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= 0.180 Angle : 0.675 11.643 11162 Z= 0.328 Chirality : 0.043 0.141 1386 Planarity : 0.003 0.029 1382 Dihedral : 4.476 49.499 1136 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.34 % Allowed : 27.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1082 helix: 1.78 (0.20), residues: 734 sheet: -2.00 (0.60), residues: 62 loop : -1.48 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 367 HIS 0.003 0.001 HIS B 469 PHE 0.017 0.002 PHE A 300 TYR 0.010 0.001 TYR B 216 ARG 0.002 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 522) hydrogen bonds : angle 4.48425 ( 1512) covalent geometry : bond 0.00383 ( 8218) covalent geometry : angle 0.67482 (11162) *********************** 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 139 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 93 time to evaluate : 0.879 Fit side-chains REVERT: A 70 MET cc_start: 0.9607 (tpp) cc_final: 0.9160 (mpp) REVERT: A 80 SER cc_start: 0.9720 (m) cc_final: 0.9328 (t) REVERT: A 140 GLU cc_start: 0.9180 (tp30) cc_final: 0.8830 (tp30) REVERT: A 182 MET cc_start: 0.9463 (tpp) cc_final: 0.9187 (tmm) REVERT: A 218 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8250 (mm) REVERT: A 323 MET cc_start: 0.8999 (ppp) cc_final: 0.8400 (ppp) REVERT: A 424 GLU cc_start: 0.9455 (tt0) cc_final: 0.9130 (tm-30) REVERT: A 437 THR cc_start: 0.9678 (OUTLIER) cc_final: 0.9309 (p) REVERT: A 541 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9027 (mm) REVERT: B 48 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9494 (mm) REVERT: B 140 GLU cc_start: 0.9170 (tp30) cc_final: 0.8905 (tp30) REVERT: B 182 MET cc_start: 0.9524 (tmm) cc_final: 0.9236 (tmm) REVERT: B 241 VAL cc_start: 0.9540 (OUTLIER) cc_final: 0.9322 (p) REVERT: B 323 MET cc_start: 0.8913 (ppp) cc_final: 0.8017 (ppp) REVERT: B 505 SER cc_start: 0.9681 (OUTLIER) cc_final: 0.9446 (p) REVERT: B 531 LEU cc_start: 0.9593 (tp) cc_final: 0.9347 (tp) outliers start: 46 outliers final: 25 residues processed: 135 average time/residue: 0.1383 time to fit residues: 28.5703 Evaluate side-chains 113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 202 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 251 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 374 LEU Chi-restraints excluded: chain A residue 383 THR 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 241 VAL Chi-restraints excluded: chain B residue 295 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 505 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN B 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.038305 restraints weight = 40847.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.039661 restraints weight = 23109.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.040653 restraints weight = 15808.787| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8218 Z= 0.124 Angle : 0.668 11.465 11162 Z= 0.312 Chirality : 0.042 0.138 1386 Planarity : 0.003 0.028 1382 Dihedral : 4.389 51.774 1136 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.29 % Allowed : 29.23 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1082 helix: 1.84 (0.20), residues: 734 sheet: -1.92 (0.59), residues: 62 loop : -1.61 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 367 HIS 0.002 0.001 HIS B 150 PHE 0.016 0.001 PHE B 277 TYR 0.010 0.001 TYR A 163 ARG 0.002 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 522) hydrogen bonds : angle 4.23693 ( 1512) covalent geometry : bond 0.00270 ( 8218) covalent geometry : angle 0.66773 (11162) *********************** 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 132 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9607 (tpp) cc_final: 0.9186 (mpp) REVERT: A 80 SER cc_start: 0.9677 (m) cc_final: 0.9259 (t) REVERT: A 140 GLU cc_start: 0.9169 (tp30) cc_final: 0.8805 (tp30) REVERT: A 182 MET cc_start: 0.9461 (tpp) cc_final: 0.9185 (tmm) REVERT: A 218 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8249 (mm) REVERT: A 323 MET cc_start: 0.9105 (ppp) cc_final: 0.8059 (ppp) REVERT: A 431 LEU cc_start: 0.9480 (tp) cc_final: 0.9271 (mt) REVERT: A 541 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8963 (mm) REVERT: B 48 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9479 (mm) REVERT: B 80 SER cc_start: 0.9582 (m) cc_final: 0.9103 (t) REVERT: B 85 MET cc_start: 0.9088 (tmm) cc_final: 0.8734 (tmm) REVERT: B 140 GLU cc_start: 0.9174 (tp30) cc_final: 0.8890 (tp30) REVERT: B 182 MET cc_start: 0.9493 (tmm) cc_final: 0.9145 (tmm) REVERT: B 241 VAL cc_start: 0.9507 (OUTLIER) cc_final: 0.9288 (p) REVERT: B 323 MET cc_start: 0.8900 (ppp) cc_final: 0.7988 (ppp) REVERT: B 339 LEU cc_start: 0.9726 (mt) cc_final: 0.9189 (pt) REVERT: B 531 LEU cc_start: 0.9578 (tp) cc_final: 0.9352 (tp) outliers start: 37 outliers final: 23 residues processed: 128 average time/residue: 0.1402 time to fit residues: 27.7509 Evaluate side-chains 114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 251 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 374 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 541 LEU 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 241 VAL Chi-restraints excluded: chain B residue 295 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** B 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.050821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.036341 restraints weight = 42906.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.037615 restraints weight = 24164.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.038562 restraints weight = 16517.472| |-----------------------------------------------------------------------------| r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8218 Z= 0.211 Angle : 0.689 10.595 11162 Z= 0.344 Chirality : 0.043 0.182 1386 Planarity : 0.003 0.028 1382 Dihedral : 4.671 59.182 1136 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.29 % Allowed : 30.39 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1082 helix: 1.83 (0.20), residues: 734 sheet: -1.88 (0.60), residues: 62 loop : -1.63 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 367 HIS 0.003 0.001 HIS A 115 PHE 0.016 0.002 PHE A 300 TYR 0.010 0.001 TYR A 167 ARG 0.002 0.000 ARG A 507 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 522) hydrogen bonds : angle 4.49342 ( 1512) covalent geometry : bond 0.00444 ( 8218) covalent geometry : angle 0.68925 (11162) *********************** 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 128 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 1.742 Fit side-chains REVERT: A 70 MET cc_start: 0.9639 (tpp) cc_final: 0.9123 (mpp) REVERT: A 80 SER cc_start: 0.9713 (m) cc_final: 0.9298 (t) REVERT: A 113 MET cc_start: 0.9488 (tmm) cc_final: 0.9105 (ppp) REVERT: A 140 GLU cc_start: 0.9209 (tp30) cc_final: 0.8844 (tp30) REVERT: A 182 MET cc_start: 0.9519 (tpp) cc_final: 0.9229 (tmm) REVERT: A 218 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8377 (mm) REVERT: A 269 GLU cc_start: 0.9543 (mp0) cc_final: 0.9102 (pm20) REVERT: A 323 MET cc_start: 0.9200 (ppp) cc_final: 0.8650 (ppp) REVERT: A 415 MET cc_start: 0.8917 (mpp) cc_final: 0.8214 (mpp) REVERT: A 420 ASP cc_start: 0.9146 (p0) cc_final: 0.8677 (p0) REVERT: A 431 LEU cc_start: 0.9536 (tp) cc_final: 0.9247 (mt) REVERT: A 437 THR cc_start: 0.9697 (OUTLIER) cc_final: 0.9348 (p) REVERT: B 48 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9508 (mm) REVERT: B 80 SER cc_start: 0.9660 (m) cc_final: 0.9220 (t) REVERT: B 113 MET cc_start: 0.9305 (tmm) cc_final: 0.9080 (ppp) REVERT: B 140 GLU cc_start: 0.9154 (tp30) cc_final: 0.8872 (tp30) REVERT: B 182 MET cc_start: 0.9569 (tmm) cc_final: 0.9242 (tmm) REVERT: B 269 GLU cc_start: 0.9497 (mp0) cc_final: 0.9081 (pm20) REVERT: B 323 MET cc_start: 0.9008 (ppp) cc_final: 0.8448 (ppp) REVERT: B 339 LEU cc_start: 0.9750 (mt) cc_final: 0.9240 (pt) REVERT: B 431 LEU cc_start: 0.9550 (tp) cc_final: 0.9334 (mt) outliers start: 37 outliers final: 23 residues processed: 127 average time/residue: 0.1717 time to fit residues: 33.9395 Evaluate side-chains 105 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 178 LEU 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 383 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 498 SER 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 217 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 447 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.3034 r_free = 0.3034 target = 0.052231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.037289 restraints weight = 41845.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.038527 restraints weight = 24162.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.039442 restraints weight = 16777.814| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8218 Z= 0.184 Angle : 0.702 10.114 11162 Z= 0.340 Chirality : 0.042 0.177 1386 Planarity : 0.003 0.032 1382 Dihedral : 4.696 57.124 1136 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.94 % Allowed : 31.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1082 helix: 1.86 (0.20), residues: 734 sheet: -1.89 (0.59), residues: 62 loop : -1.61 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 367 HIS 0.002 0.001 HIS B 469 PHE 0.015 0.002 PHE A 300 TYR 0.009 0.001 TYR A 289 ARG 0.001 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 522) hydrogen bonds : angle 4.41019 ( 1512) covalent geometry : bond 0.00393 ( 8218) covalent geometry : angle 0.70207 (11162) *********************** 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 124 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.876 Fit side-chains REVERT: A 70 MET cc_start: 0.9632 (tpp) cc_final: 0.9146 (mpp) REVERT: A 80 SER cc_start: 0.9691 (m) cc_final: 0.9277 (t) REVERT: A 140 GLU cc_start: 0.9198 (tp30) cc_final: 0.8830 (tp30) REVERT: A 182 MET cc_start: 0.9540 (tpp) cc_final: 0.9235 (tmm) REVERT: A 218 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8354 (mm) REVERT: A 269 GLU cc_start: 0.9539 (mp0) cc_final: 0.9084 (pm20) REVERT: A 323 MET cc_start: 0.9257 (ppp) cc_final: 0.8778 (ppp) REVERT: A 415 MET cc_start: 0.8936 (mpp) cc_final: 0.8184 (mpp) REVERT: A 431 LEU cc_start: 0.9526 (tp) cc_final: 0.9237 (mt) REVERT: A 437 THR cc_start: 0.9676 (OUTLIER) cc_final: 0.9325 (p) REVERT: A 480 MET cc_start: 0.9236 (ptm) cc_final: 0.8441 (ppp) REVERT: A 482 MET cc_start: 0.6748 (mtt) cc_final: 0.6367 (mtt) REVERT: B 48 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9487 (mm) REVERT: B 80 SER cc_start: 0.9643 (m) cc_final: 0.9214 (t) REVERT: B 85 MET cc_start: 0.9113 (tmm) cc_final: 0.8803 (tmm) REVERT: B 140 GLU cc_start: 0.9144 (tp30) cc_final: 0.8859 (tp30) REVERT: B 182 MET cc_start: 0.9551 (tmm) cc_final: 0.9181 (tmm) REVERT: B 203 MET cc_start: 0.9412 (mmp) cc_final: 0.9081 (mmp) REVERT: B 269 GLU cc_start: 0.9498 (mp0) cc_final: 0.9076 (pm20) REVERT: B 323 MET cc_start: 0.9086 (ppp) cc_final: 0.8603 (ppp) REVERT: B 431 LEU cc_start: 0.9530 (tp) cc_final: 0.9319 (mt) REVERT: B 480 MET cc_start: 0.9256 (ptm) cc_final: 0.8855 (pmm) outliers start: 34 outliers final: 26 residues processed: 123 average time/residue: 0.1378 time to fit residues: 25.8763 Evaluate side-chains 113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 178 LEU 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 374 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 464 ILE 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 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 295 VAL Chi-restraints excluded: chain B residue 362 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3034 r_free = 0.3034 target = 0.051389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.036846 restraints weight = 42609.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.038137 restraints weight = 24316.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.039081 restraints weight = 16704.892| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.5019 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= 0.159 Angle : 0.692 11.683 11162 Z= 0.333 Chirality : 0.042 0.155 1386 Planarity : 0.003 0.031 1382 Dihedral : 4.628 54.184 1136 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.83 % Allowed : 32.83 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1082 helix: 1.91 (0.20), residues: 736 sheet: -1.91 (0.58), residues: 62 loop : -1.62 (0.32), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 367 HIS 0.002 0.001 HIS B 150 PHE 0.015 0.001 PHE A 300 TYR 0.009 0.001 TYR A 289 ARG 0.001 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 522) hydrogen bonds : angle 4.39219 ( 1512) covalent geometry : bond 0.00344 ( 8218) covalent geometry : angle 0.69166 (11162) *********************** 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 121 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 2.512 Fit side-chains REVERT: A 70 MET cc_start: 0.9624 (tpp) cc_final: 0.9130 (mpp) REVERT: A 80 SER cc_start: 0.9678 (m) cc_final: 0.9259 (t) REVERT: A 140 GLU cc_start: 0.9189 (tp30) cc_final: 0.8819 (tp30) REVERT: A 182 MET cc_start: 0.9534 (tpp) cc_final: 0.9196 (tmm) REVERT: A 218 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 269 GLU cc_start: 0.9527 (mp0) cc_final: 0.9075 (pm20) REVERT: A 323 MET cc_start: 0.9277 (ppp) cc_final: 0.8755 (ppp) REVERT: A 415 MET cc_start: 0.8947 (mpp) cc_final: 0.8202 (mpp) REVERT: A 431 LEU cc_start: 0.9512 (tp) cc_final: 0.9250 (mt) REVERT: A 437 THR cc_start: 0.9662 (OUTLIER) cc_final: 0.9313 (p) REVERT: B 48 LEU cc_start: 0.9738 (OUTLIER) cc_final: 0.9482 (mm) REVERT: B 55 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8584 (p90) REVERT: B 80 SER cc_start: 0.9641 (m) cc_final: 0.9208 (t) REVERT: B 85 MET cc_start: 0.9099 (tmm) cc_final: 0.8789 (tmm) REVERT: B 140 GLU cc_start: 0.9122 (tp30) cc_final: 0.8828 (tp30) REVERT: B 182 MET cc_start: 0.9543 (tmm) cc_final: 0.9160 (tmm) REVERT: B 269 GLU cc_start: 0.9500 (mp0) cc_final: 0.9085 (pm20) REVERT: B 323 MET cc_start: 0.9070 (ppp) cc_final: 0.8617 (ppp) REVERT: B 415 MET cc_start: 0.8903 (mpp) cc_final: 0.8106 (mpp) REVERT: B 480 MET cc_start: 0.9285 (ptm) cc_final: 0.8900 (pmm) REVERT: B 531 LEU cc_start: 0.9559 (tp) cc_final: 0.9326 (tp) outliers start: 33 outliers final: 25 residues processed: 120 average time/residue: 0.2185 time to fit residues: 40.5569 Evaluate side-chains 113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 68 PHE Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 LEU 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 437 THR Chi-restraints excluded: chain A residue 456 SER 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 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 295 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 447 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.053501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.038955 restraints weight = 41903.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.040297 restraints weight = 23970.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.041241 restraints weight = 16437.303| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.5107 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= 0.123 Angle : 0.728 12.339 11162 Z= 0.337 Chirality : 0.042 0.157 1386 Planarity : 0.003 0.033 1382 Dihedral : 4.584 52.711 1136 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.71 % Allowed : 33.29 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1082 helix: 2.02 (0.20), residues: 730 sheet: -1.78 (0.59), residues: 62 loop : -1.49 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 367 HIS 0.003 0.000 HIS B 150 PHE 0.014 0.001 PHE A 300 TYR 0.008 0.001 TYR A 289 ARG 0.002 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 522) hydrogen bonds : angle 4.24141 ( 1512) covalent geometry : bond 0.00269 ( 8218) covalent geometry : angle 0.72753 (11162) *********************** 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 123 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.912 Fit side-chains REVERT: A 70 MET cc_start: 0.9590 (tpp) cc_final: 0.9131 (mpp) REVERT: A 80 SER cc_start: 0.9645 (m) cc_final: 0.9204 (t) REVERT: A 113 MET cc_start: 0.9278 (tmm) cc_final: 0.8996 (ppp) REVERT: A 140 GLU cc_start: 0.9142 (tp30) cc_final: 0.8754 (tp30) REVERT: A 182 MET cc_start: 0.9512 (tpp) cc_final: 0.9251 (tpp) REVERT: A 218 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 323 MET cc_start: 0.9271 (ppp) cc_final: 0.8646 (ppp) REVERT: A 415 MET cc_start: 0.8906 (mpp) cc_final: 0.8145 (mpp) REVERT: A 431 LEU cc_start: 0.9473 (tp) cc_final: 0.9266 (mt) REVERT: B 48 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9466 (mm) REVERT: B 55 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8714 (p90) REVERT: B 80 SER cc_start: 0.9609 (m) cc_final: 0.9158 (t) REVERT: B 113 MET cc_start: 0.9290 (tmm) cc_final: 0.9033 (ppp) REVERT: B 140 GLU cc_start: 0.9118 (tp30) cc_final: 0.8825 (tp30) REVERT: B 182 MET cc_start: 0.9531 (tmm) cc_final: 0.9115 (tmm) REVERT: B 269 GLU cc_start: 0.9519 (mp0) cc_final: 0.9087 (pm20) REVERT: B 323 MET cc_start: 0.9045 (ppp) cc_final: 0.8530 (ppp) REVERT: B 480 MET cc_start: 0.9232 (ptm) cc_final: 0.8911 (pmm) REVERT: B 531 LEU cc_start: 0.9535 (tp) cc_final: 0.9310 (tp) outliers start: 32 outliers final: 23 residues processed: 120 average time/residue: 0.1405 time to fit residues: 25.6084 Evaluate side-chains 113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 178 LEU 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 396 THR Chi-restraints excluded: chain A residue 456 SER 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 283 THR 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 539 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 95 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 25 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.053871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.039152 restraints weight = 41896.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.040527 restraints weight = 23903.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.041588 restraints weight = 16419.645| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8218 Z= 0.123 Angle : 0.750 12.823 11162 Z= 0.343 Chirality : 0.043 0.164 1386 Planarity : 0.003 0.032 1382 Dihedral : 4.550 51.839 1136 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.90 % Allowed : 34.69 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1082 helix: 1.98 (0.20), residues: 732 sheet: -1.70 (0.58), residues: 62 loop : -1.42 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 367 HIS 0.003 0.000 HIS B 150 PHE 0.014 0.001 PHE A 300 TYR 0.008 0.001 TYR B 289 ARG 0.002 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 522) hydrogen bonds : angle 4.17904 ( 1512) covalent geometry : bond 0.00274 ( 8218) covalent geometry : angle 0.74961 (11162) ********************** 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 111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9603 (tpp) cc_final: 0.9107 (mpp) REVERT: A 80 SER cc_start: 0.9647 (m) cc_final: 0.9203 (t) REVERT: A 113 MET cc_start: 0.9280 (tmm) cc_final: 0.9007 (ppp) REVERT: A 140 GLU cc_start: 0.9115 (tp30) cc_final: 0.8720 (tp30) REVERT: A 218 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8288 (mm) REVERT: A 269 GLU cc_start: 0.9530 (mp0) cc_final: 0.9152 (pm20) REVERT: A 323 MET cc_start: 0.9239 (ppp) cc_final: 0.8653 (ppp) REVERT: A 396 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9187 (p) REVERT: A 415 MET cc_start: 0.8913 (mpp) cc_final: 0.8147 (mpp) REVERT: A 456 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8794 (p) REVERT: B 48 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9446 (mm) REVERT: B 55 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8730 (p90) REVERT: B 70 MET cc_start: 0.9646 (tpp) cc_final: 0.9085 (mpp) REVERT: B 80 SER cc_start: 0.9605 (m) cc_final: 0.9147 (t) REVERT: B 113 MET cc_start: 0.9296 (tmm) cc_final: 0.9048 (ppp) REVERT: B 140 GLU cc_start: 0.9097 (tp30) cc_final: 0.8793 (tp30) REVERT: B 182 MET cc_start: 0.9525 (tmm) cc_final: 0.9104 (tmm) REVERT: B 251 MET cc_start: 0.9597 (mmp) cc_final: 0.9378 (mmt) REVERT: B 269 GLU cc_start: 0.9520 (mp0) cc_final: 0.9077 (pm20) REVERT: B 323 MET cc_start: 0.9014 (ppp) cc_final: 0.8444 (ppp) REVERT: B 480 MET cc_start: 0.9226 (ptm) cc_final: 0.8895 (pmm) outliers start: 25 outliers final: 17 residues processed: 111 average time/residue: 0.1533 time to fit residues: 26.0799 Evaluate side-chains 105 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 178 LEU 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 396 THR Chi-restraints excluded: chain A residue 456 SER 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 132 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 539 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 = 0.3070 r_free = 0.3070 target = 0.052757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.038033 restraints weight = 42011.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.039365 restraints weight = 23979.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.040247 restraints weight = 16444.915| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8218 Z= 0.143 Angle : 0.767 14.369 11162 Z= 0.352 Chirality : 0.043 0.164 1386 Planarity : 0.003 0.031 1382 Dihedral : 4.593 50.827 1136 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.55 % Allowed : 35.03 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1082 helix: 1.92 (0.20), residues: 736 sheet: -1.75 (0.57), residues: 62 loop : -1.38 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 367 HIS 0.002 0.001 HIS B 150 PHE 0.022 0.001 PHE A 473 TYR 0.008 0.001 TYR A 167 ARG 0.001 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 522) hydrogen bonds : angle 4.21532 ( 1512) covalent geometry : bond 0.00317 ( 8218) covalent geometry : angle 0.76698 (11162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.84 seconds wall clock time: 43 minutes 33.97 seconds (2613.97 seconds total)