Starting phenix.real_space_refine on Mon Nov 17 23:53:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dz7_8931/11_2025/6dz7_8931.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dz7_8931/11_2025/6dz7_8931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dz7_8931/11_2025/6dz7_8931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dz7_8931/11_2025/6dz7_8931.map" model { file = "/net/cci-nas-00/data/ceres_data/6dz7_8931/11_2025/6dz7_8931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dz7_8931/11_2025/6dz7_8931.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 38 5.16 5 C 6098 2.51 5 N 1534 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9284 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 4642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4642 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 26, 'TRANS': 547} Chain breaks: 9 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 5, 'GLU:plan': 5, 'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Restraints were copied for chains: A Time building chain proxies: 3.33, per 1000 atoms: 0.36 Number of scatterers: 9284 At special positions: 0 Unit cell: (129.34, 75.6309, 100.841, 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 38 16.00 O 1614 8.00 N 1534 7.00 C 6098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 249.0 milliseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 2 sheets defined 69.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 68 through 86 removed outlier: 3.625A pdb=" N TYR B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 117 Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.671A pdb=" N THR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 200 removed outlier: 4.539A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Proline residue: B 194 - end of helix Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.619A pdb=" N THR B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 312 removed outlier: 3.549A pdb=" N TYR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Proline residue: B 285 - end of helix Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 322 through 349 removed outlier: 3.815A pdb=" N ILE B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.919A pdb=" N ALA B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 386 removed outlier: 3.781A pdb=" N LYS B 359 " --> pdb=" O GLN B 355 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 425 through 448 removed outlier: 4.054A pdb=" N ILE B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALA B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLN B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 502 removed outlier: 3.516A pdb=" N GLU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 525 removed outlier: 3.533A pdb=" N LEU B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 553 removed outlier: 5.616A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 591 removed outlier: 3.852A pdb=" N TYR B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 635 removed outlier: 3.874A pdb=" N LEU B 611 " --> pdb=" O CYS B 607 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 658 removed outlier: 4.412A pdb=" N GLU B 646 " --> pdb=" O ARG B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 727 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 68 through 86 removed outlier: 3.626A pdb=" N TYR A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 162 through 172 removed outlier: 3.670A pdb=" N THR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 200 removed outlier: 4.540A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.619A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 312 removed outlier: 3.549A pdb=" N TYR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 322 through 349 removed outlier: 3.815A pdb=" N ILE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.919A pdb=" N ALA A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 386 removed outlier: 3.781A pdb=" N LYS A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 425 through 448 removed outlier: 4.054A pdb=" N ILE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLN A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 502 removed outlier: 3.516A pdb=" N GLU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 525 removed outlier: 3.532A pdb=" N LEU A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 553 removed outlier: 5.616A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER A 546 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 removed outlier: 3.852A pdb=" N TYR A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 635 removed outlier: 3.874A pdb=" N LEU A 611 " --> pdb=" O CYS A 607 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 658 removed outlier: 4.411A pdb=" N GLU A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 21 removed outlier: 7.768A pdb=" N TYR B 18 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG B 65 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 20 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE B 63 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N VAL B 62 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL B 52 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL B 64 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR B 50 " --> pdb=" O VAL B 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 7.768A pdb=" N TYR A 18 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG A 65 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE A 20 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE A 63 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N VAL A 62 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N VAL A 52 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 64 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR A 50 " --> pdb=" O VAL A 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 570 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2703 1.34 - 1.46: 1989 1.46 - 1.57: 4770 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 9518 Sorted by residual: bond pdb=" C VAL B 448 " pdb=" N PRO B 449 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.72e+00 bond pdb=" C VAL A 448 " pdb=" N PRO A 449 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.69e+00 bond pdb=" CB ASN A 370 " pdb=" CG ASN A 370 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.45e+00 bond pdb=" CB ASN B 370 " pdb=" CG ASN B 370 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.41e+00 bond pdb=" CG1 ILE A 221 " pdb=" CD1 ILE A 221 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.30e+00 ... (remaining 9513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 12216 2.39 - 4.78: 564 4.78 - 7.17: 113 7.17 - 9.56: 35 9.56 - 11.95: 8 Bond angle restraints: 12936 Sorted by residual: angle pdb=" N ILE B 323 " pdb=" CA ILE B 323 " pdb=" C ILE B 323 " ideal model delta sigma weight residual 108.88 120.83 -11.95 2.16e+00 2.14e-01 3.06e+01 angle pdb=" N ILE A 323 " pdb=" CA ILE A 323 " pdb=" C ILE A 323 " ideal model delta sigma weight residual 108.88 120.81 -11.93 2.16e+00 2.14e-01 3.05e+01 angle pdb=" C GLU B 132 " pdb=" N TRP B 133 " pdb=" CA TRP B 133 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.93e+01 angle pdb=" C GLU A 132 " pdb=" N TRP A 133 " pdb=" CA TRP A 133 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.93e+01 angle pdb=" N GLU B 94 " pdb=" CA GLU B 94 " pdb=" C GLU B 94 " ideal model delta sigma weight residual 109.81 119.61 -9.80 2.21e+00 2.05e-01 1.97e+01 ... (remaining 12931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 5192 15.89 - 31.77: 300 31.77 - 47.66: 94 47.66 - 63.54: 2 63.54 - 79.43: 8 Dihedral angle restraints: 5596 sinusoidal: 2200 harmonic: 3396 Sorted by residual: dihedral pdb=" CA TRP A 155 " pdb=" C TRP A 155 " pdb=" N SER A 156 " pdb=" CA SER A 156 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA TRP B 155 " pdb=" C TRP B 155 " pdb=" N SER B 156 " pdb=" CA SER B 156 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ILE A 27 " pdb=" C ILE A 27 " pdb=" N ASP A 28 " pdb=" CA ASP A 28 " ideal model delta harmonic sigma weight residual 180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 5593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1019 0.060 - 0.121: 347 0.121 - 0.181: 86 0.181 - 0.241: 18 0.241 - 0.302: 4 Chirality restraints: 1474 Sorted by residual: chirality pdb=" CB VAL B 117 " pdb=" CA VAL B 117 " pdb=" CG1 VAL B 117 " pdb=" CG2 VAL B 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB VAL A 117 " pdb=" CA VAL A 117 " pdb=" CG1 VAL A 117 " pdb=" CG2 VAL A 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE B 323 " pdb=" CA ILE B 323 " pdb=" CG1 ILE B 323 " pdb=" CG2 ILE B 323 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1471 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 637 " 0.063 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO B 638 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 638 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 638 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 637 " -0.063 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO A 638 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 372 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ILE B 372 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE B 372 " 0.021 2.00e-02 2.50e+03 pdb=" N THR B 373 " 0.019 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2850 2.82 - 3.34: 9208 3.34 - 3.86: 15105 3.86 - 4.38: 15828 4.38 - 4.90: 26691 Nonbonded interactions: 69682 Sorted by model distance: nonbonded pdb=" O TYR B 432 " pdb=" OG1 THR B 436 " model vdw 2.305 3.040 nonbonded pdb=" O TYR A 432 " pdb=" OG1 THR A 436 " model vdw 2.305 3.040 nonbonded pdb=" OD1 ASP B 510 " pdb=" NH2 ARG B 513 " model vdw 2.316 3.120 nonbonded pdb=" OD1 ASP A 510 " pdb=" NH2 ARG A 513 " model vdw 2.316 3.120 nonbonded pdb=" O MET A 152 " pdb=" NH2 ARG A 545 " model vdw 2.357 3.120 ... (remaining 69677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.030 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.760 Find NCS groups from input model: 0.060 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.010 0.087 9518 Z= 0.422 Angle : 1.252 11.953 12936 Z= 0.671 Chirality : 0.066 0.302 1474 Planarity : 0.009 0.097 1600 Dihedral : 11.475 79.430 3376 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 0.20 % Allowed : 4.67 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.21), residues: 1108 helix: -1.69 (0.15), residues: 784 sheet: -5.00 (0.81), residues: 20 loop : -4.31 (0.28), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 89 TYR 0.026 0.003 TYR B 187 PHE 0.021 0.003 PHE B 140 TRP 0.037 0.006 TRP B 227 HIS 0.017 0.005 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00966 ( 9518) covalent geometry : angle 1.25181 (12936) hydrogen bonds : bond 0.10968 ( 570) hydrogen bonds : angle 5.85408 ( 1710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7804 (p90) cc_final: 0.7565 (p90) REVERT: B 335 MET cc_start: 0.8369 (mmm) cc_final: 0.8119 (mmt) REVERT: A 192 MET cc_start: 0.8079 (ptt) cc_final: 0.7835 (ptm) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.1205 time to fit residues: 18.5487 Evaluate side-chains 44 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 176 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 78 GLN A 176 HIS A 280 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.059831 restraints weight = 43045.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061264 restraints weight = 25981.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062262 restraints weight = 18373.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.062957 restraints weight = 14454.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063416 restraints weight = 12245.300| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9518 Z= 0.167 Angle : 0.765 9.226 12936 Z= 0.394 Chirality : 0.044 0.231 1474 Planarity : 0.006 0.079 1600 Dihedral : 5.716 25.304 1248 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 1.93 % Allowed : 9.23 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.25), residues: 1108 helix: -0.10 (0.18), residues: 794 sheet: -4.87 (0.79), residues: 20 loop : -4.03 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 89 TYR 0.017 0.001 TYR A 180 PHE 0.019 0.001 PHE A 616 TRP 0.032 0.003 TRP A 706 HIS 0.004 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9518) covalent geometry : angle 0.76465 (12936) hydrogen bonds : bond 0.05823 ( 570) hydrogen bonds : angle 4.68004 ( 1710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.276 Fit side-chains REVERT: B 286 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8054 (t80) REVERT: B 335 MET cc_start: 0.8081 (mmm) cc_final: 0.7850 (mmt) REVERT: B 514 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7667 (mp0) REVERT: B 641 ARG cc_start: 0.8478 (ttt90) cc_final: 0.8197 (ptt90) REVERT: A 641 ARG cc_start: 0.8619 (ttt90) cc_final: 0.7892 (ptt90) outliers start: 19 outliers final: 7 residues processed: 84 average time/residue: 0.0964 time to fit residues: 11.4842 Evaluate side-chains 57 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 588 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 99 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.072098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060932 restraints weight = 42877.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.062344 restraints weight = 25977.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.063380 restraints weight = 18353.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.064038 restraints weight = 14238.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064537 restraints weight = 12026.210| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9518 Z= 0.138 Angle : 0.685 8.913 12936 Z= 0.345 Chirality : 0.041 0.192 1474 Planarity : 0.006 0.079 1600 Dihedral : 5.046 22.578 1248 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 3.55 % Allowed : 9.63 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.26), residues: 1108 helix: 0.59 (0.19), residues: 796 sheet: -4.66 (0.78), residues: 20 loop : -3.82 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 425 TYR 0.011 0.001 TYR B 180 PHE 0.014 0.001 PHE A 616 TRP 0.020 0.002 TRP A 541 HIS 0.003 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9518) covalent geometry : angle 0.68460 (12936) hydrogen bonds : bond 0.04820 ( 570) hydrogen bonds : angle 4.32530 ( 1710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 0.304 Fit side-chains REVERT: B 192 MET cc_start: 0.8380 (ttp) cc_final: 0.8076 (ttp) REVERT: B 545 ARG cc_start: 0.7677 (mmp80) cc_final: 0.6965 (mmt180) REVERT: A 42 GLU cc_start: 0.8797 (tp30) cc_final: 0.8569 (tp30) REVERT: A 294 LEU cc_start: 0.9396 (tp) cc_final: 0.9183 (tt) outliers start: 35 outliers final: 13 residues processed: 95 average time/residue: 0.0898 time to fit residues: 12.0856 Evaluate side-chains 69 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.0970 chunk 81 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 22 optimal weight: 0.0060 overall best weight: 2.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058053 restraints weight = 43997.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059360 restraints weight = 27029.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060277 restraints weight = 19399.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.060853 restraints weight = 15384.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061335 restraints weight = 13240.359| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9518 Z= 0.222 Angle : 0.739 13.646 12936 Z= 0.377 Chirality : 0.044 0.195 1474 Planarity : 0.006 0.068 1600 Dihedral : 5.126 24.934 1248 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 2.43 % Allowed : 11.46 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.27), residues: 1108 helix: 0.93 (0.19), residues: 796 sheet: -4.47 (0.82), residues: 20 loop : -3.58 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 562 TYR 0.015 0.002 TYR B 506 PHE 0.018 0.002 PHE B 433 TRP 0.022 0.002 TRP B 706 HIS 0.006 0.002 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 9518) covalent geometry : angle 0.73872 (12936) hydrogen bonds : bond 0.05352 ( 570) hydrogen bonds : angle 4.42666 ( 1710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.315 Fit side-chains REVERT: B 192 MET cc_start: 0.8503 (ttp) cc_final: 0.8206 (ttp) REVERT: B 232 GLU cc_start: 0.8600 (tp30) cc_final: 0.8393 (tp30) REVERT: B 515 MET cc_start: 0.8434 (tmm) cc_final: 0.8195 (tmm) REVERT: B 524 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8825 (mp) REVERT: A 340 LEU cc_start: 0.9106 (tt) cc_final: 0.8865 (mt) REVERT: A 524 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8718 (mp) outliers start: 24 outliers final: 17 residues processed: 70 average time/residue: 0.0817 time to fit residues: 8.5254 Evaluate side-chains 67 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.071527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060257 restraints weight = 43178.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.061615 restraints weight = 26742.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062566 restraints weight = 19201.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063162 restraints weight = 15244.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.063618 restraints weight = 13100.008| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9518 Z= 0.133 Angle : 0.669 16.259 12936 Z= 0.330 Chirality : 0.040 0.196 1474 Planarity : 0.005 0.063 1600 Dihedral : 4.758 21.985 1248 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.33 % Allowed : 11.87 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.27), residues: 1108 helix: 1.16 (0.19), residues: 792 sheet: -4.34 (0.81), residues: 20 loop : -3.63 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 545 TYR 0.010 0.001 TYR B 180 PHE 0.012 0.001 PHE A 616 TRP 0.015 0.002 TRP A 541 HIS 0.003 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9518) covalent geometry : angle 0.66932 (12936) hydrogen bonds : bond 0.04558 ( 570) hydrogen bonds : angle 4.15024 ( 1710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.351 Fit side-chains REVERT: B 192 MET cc_start: 0.8494 (ttp) cc_final: 0.8187 (ttp) REVERT: B 515 MET cc_start: 0.8378 (tmm) cc_final: 0.8104 (tmm) REVERT: A 340 LEU cc_start: 0.9060 (tt) cc_final: 0.8845 (mt) REVERT: A 545 ARG cc_start: 0.7810 (mmp-170) cc_final: 0.6413 (ptp-170) outliers start: 23 outliers final: 17 residues processed: 74 average time/residue: 0.0882 time to fit residues: 9.6296 Evaluate side-chains 64 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.069004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.057734 restraints weight = 43820.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059020 restraints weight = 27142.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059909 restraints weight = 19606.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060494 restraints weight = 15681.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.060924 restraints weight = 13526.172| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9518 Z= 0.216 Angle : 0.712 10.742 12936 Z= 0.362 Chirality : 0.043 0.188 1474 Planarity : 0.005 0.067 1600 Dihedral : 4.861 23.541 1248 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 2.94 % Allowed : 11.56 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 1108 helix: 1.21 (0.19), residues: 796 sheet: -4.26 (0.82), residues: 20 loop : -3.36 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 89 TYR 0.017 0.002 TYR A 506 PHE 0.012 0.001 PHE A 173 TRP 0.017 0.002 TRP B 155 HIS 0.005 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9518) covalent geometry : angle 0.71242 (12936) hydrogen bonds : bond 0.05095 ( 570) hydrogen bonds : angle 4.31857 ( 1710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 46 time to evaluate : 0.358 Fit side-chains REVERT: B 192 MET cc_start: 0.8546 (ttp) cc_final: 0.8248 (ttp) REVERT: A 340 LEU cc_start: 0.9098 (tt) cc_final: 0.8860 (mt) REVERT: A 524 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8758 (mp) REVERT: A 545 ARG cc_start: 0.7929 (mmp-170) cc_final: 0.6552 (ptp-170) outliers start: 29 outliers final: 23 residues processed: 71 average time/residue: 0.0945 time to fit residues: 9.6328 Evaluate side-chains 68 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 52 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.069323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058033 restraints weight = 43716.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059339 restraints weight = 27081.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060251 restraints weight = 19472.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060797 restraints weight = 15490.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061259 restraints weight = 13389.027| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9518 Z= 0.183 Angle : 0.697 10.444 12936 Z= 0.351 Chirality : 0.042 0.194 1474 Planarity : 0.005 0.063 1600 Dihedral : 4.829 22.677 1248 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.64 % Allowed : 12.88 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.27), residues: 1108 helix: 1.33 (0.19), residues: 792 sheet: -4.27 (0.82), residues: 20 loop : -3.34 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 89 TYR 0.013 0.001 TYR A 506 PHE 0.015 0.001 PHE A 253 TRP 0.018 0.002 TRP B 541 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9518) covalent geometry : angle 0.69746 (12936) hydrogen bonds : bond 0.04954 ( 570) hydrogen bonds : angle 4.25419 ( 1710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.340 Fit side-chains REVERT: B 192 MET cc_start: 0.8543 (ttp) cc_final: 0.8247 (ttp) REVERT: B 524 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8751 (mp) REVERT: A 340 LEU cc_start: 0.9138 (tt) cc_final: 0.8885 (mt) REVERT: A 524 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8744 (mp) REVERT: A 545 ARG cc_start: 0.7858 (mmp-170) cc_final: 0.6612 (ptp-170) outliers start: 26 outliers final: 21 residues processed: 68 average time/residue: 0.0805 time to fit residues: 8.2735 Evaluate side-chains 65 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.070766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059556 restraints weight = 43198.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060929 restraints weight = 26419.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061896 restraints weight = 18735.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062467 restraints weight = 14760.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062977 restraints weight = 12654.859| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9518 Z= 0.134 Angle : 0.652 9.935 12936 Z= 0.324 Chirality : 0.040 0.188 1474 Planarity : 0.005 0.061 1600 Dihedral : 4.555 22.449 1248 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 2.23 % Allowed : 13.18 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.27), residues: 1108 helix: 1.50 (0.19), residues: 792 sheet: -4.34 (0.81), residues: 20 loop : -3.35 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 641 TYR 0.010 0.001 TYR B 180 PHE 0.012 0.001 PHE A 549 TRP 0.016 0.001 TRP A 541 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9518) covalent geometry : angle 0.65173 (12936) hydrogen bonds : bond 0.04338 ( 570) hydrogen bonds : angle 4.07054 ( 1710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8521 (ttp) cc_final: 0.8220 (ttp) REVERT: B 524 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8706 (mp) REVERT: B 709 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: A 152 MET cc_start: 0.8095 (tpt) cc_final: 0.7867 (ttt) REVERT: A 545 ARG cc_start: 0.7660 (mmp-170) cc_final: 0.6556 (ptp-170) outliers start: 22 outliers final: 19 residues processed: 68 average time/residue: 0.0843 time to fit residues: 8.6566 Evaluate side-chains 65 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 103 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.069597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058327 restraints weight = 43721.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059626 restraints weight = 26983.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060445 restraints weight = 19427.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061088 restraints weight = 15702.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061448 restraints weight = 13457.114| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9518 Z= 0.193 Angle : 0.690 8.985 12936 Z= 0.348 Chirality : 0.042 0.193 1474 Planarity : 0.005 0.062 1600 Dihedral : 4.643 22.483 1248 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 2.54 % Allowed : 12.98 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.27), residues: 1108 helix: 1.52 (0.19), residues: 792 sheet: -4.17 (0.85), residues: 20 loop : -3.22 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 710 TYR 0.013 0.001 TYR A 506 PHE 0.012 0.001 PHE B 615 TRP 0.040 0.002 TRP B 706 HIS 0.005 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9518) covalent geometry : angle 0.68980 (12936) hydrogen bonds : bond 0.04742 ( 570) hydrogen bonds : angle 4.18249 ( 1710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8507 (ttp) cc_final: 0.8210 (ttp) REVERT: B 294 LEU cc_start: 0.9355 (tp) cc_final: 0.9151 (tt) REVERT: B 524 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8775 (mp) REVERT: A 524 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8740 (mp) REVERT: A 545 ARG cc_start: 0.7845 (mmp-170) cc_final: 0.6751 (ptp-170) outliers start: 25 outliers final: 22 residues processed: 66 average time/residue: 0.0799 time to fit residues: 8.1493 Evaluate side-chains 66 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 109 optimal weight: 0.0980 chunk 79 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.069950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058710 restraints weight = 43604.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.060021 restraints weight = 26748.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060926 restraints weight = 19230.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061467 restraints weight = 15352.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061902 restraints weight = 13313.225| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9518 Z= 0.161 Angle : 0.679 10.848 12936 Z= 0.339 Chirality : 0.041 0.195 1474 Planarity : 0.005 0.062 1600 Dihedral : 4.627 22.478 1248 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.54 % Allowed : 13.08 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.27), residues: 1108 helix: 1.54 (0.19), residues: 792 sheet: -4.13 (0.86), residues: 20 loop : -3.23 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 545 TYR 0.011 0.001 TYR A 506 PHE 0.011 0.001 PHE B 615 TRP 0.033 0.002 TRP B 706 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9518) covalent geometry : angle 0.67886 (12936) hydrogen bonds : bond 0.04636 ( 570) hydrogen bonds : angle 4.13325 ( 1710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8491 (ttp) cc_final: 0.8197 (ttp) REVERT: B 524 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8779 (mp) REVERT: B 709 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: A 545 ARG cc_start: 0.7690 (mmp-170) cc_final: 0.6561 (ptp-170) outliers start: 25 outliers final: 23 residues processed: 67 average time/residue: 0.0783 time to fit residues: 8.0775 Evaluate side-chains 69 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.070545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059369 restraints weight = 42741.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060717 restraints weight = 26319.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061652 restraints weight = 18738.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062264 restraints weight = 14873.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062705 restraints weight = 12734.624| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9518 Z= 0.133 Angle : 0.658 9.171 12936 Z= 0.327 Chirality : 0.041 0.195 1474 Planarity : 0.005 0.061 1600 Dihedral : 4.522 21.584 1248 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.33 % Allowed : 13.39 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.27), residues: 1108 helix: 1.60 (0.19), residues: 792 sheet: -4.02 (0.86), residues: 20 loop : -3.23 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 641 TYR 0.010 0.001 TYR B 180 PHE 0.010 0.001 PHE B 549 TRP 0.030 0.002 TRP B 706 HIS 0.003 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9518) covalent geometry : angle 0.65816 (12936) hydrogen bonds : bond 0.04406 ( 570) hydrogen bonds : angle 4.04430 ( 1710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.89 seconds wall clock time: 22 minutes 16.64 seconds (1336.64 seconds total)