Starting phenix.real_space_refine on Wed Apr 30 07:55:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dz7_8931/04_2025/6dz7_8931.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dz7_8931/04_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_8931/04_2025/6dz7_8931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dz7_8931/04_2025/6dz7_8931.map" model { file = "/net/cci-nas-00/data/ceres_data/6dz7_8931/04_2025/6dz7_8931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dz7_8931/04_2025/6dz7_8931.cif" } resolution = 3.89 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= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9284 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Restraints were copied for chains: B Time building chain proxies: 8.80, per 1000 atoms: 0.95 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: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.78 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: 2.31 Time building geometry restraints manager: 2.44 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: 0.05 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: 1.050 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.140 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.950 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.037 0.006 TRP B 227 HIS 0.017 0.005 HIS B 130 PHE 0.021 0.003 PHE B 140 TYR 0.026 0.003 TYR B 187 ARG 0.012 0.002 ARG B 89 Details of bonding type rmsd hydrogen bonds : bond 0.10968 ( 570) hydrogen bonds : angle 5.85408 ( 1710) covalent geometry : bond 0.00966 ( 9518) covalent geometry : angle 1.25181 (12936) *********************** 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 : 1.111 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: 0.2871 time to fit residues: 44.5853 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 : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.071581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060326 restraints weight = 42323.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061718 restraints weight = 25943.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.062716 restraints weight = 18521.881| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9518 Z= 0.161 Angle : 0.753 8.968 12936 Z= 0.388 Chirality : 0.043 0.242 1474 Planarity : 0.006 0.077 1600 Dihedral : 5.661 25.289 1248 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 1.93 % Allowed : 9.03 % Favored : 89.05 % 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: -1.81 (0.25), residues: 1108 helix: -0.07 (0.18), residues: 794 sheet: -4.88 (0.79), residues: 20 loop : -4.02 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 706 HIS 0.004 0.001 HIS A 619 PHE 0.020 0.001 PHE A 616 TYR 0.017 0.001 TYR A 180 ARG 0.005 0.001 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.05693 ( 570) hydrogen bonds : angle 4.64170 ( 1710) covalent geometry : bond 0.00329 ( 9518) covalent geometry : angle 0.75294 (12936) *********************** 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 91 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.003 Fit side-chains REVERT: B 286 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8056 (t80) REVERT: B 335 MET cc_start: 0.8048 (mmm) cc_final: 0.7837 (mmt) REVERT: B 514 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7733 (mp0) REVERT: B 545 ARG cc_start: 0.8271 (mmp-170) cc_final: 0.7997 (mmp-170) REVERT: B 641 ARG cc_start: 0.8462 (ttt90) cc_final: 0.8260 (ptt-90) REVERT: A 641 ARG cc_start: 0.8647 (ttt90) cc_final: 0.7943 (ptt90) outliers start: 19 outliers final: 7 residues processed: 88 average time/residue: 0.2271 time to fit residues: 28.0264 Evaluate side-chains 58 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 79 optimal weight: 0.0470 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 78 optimal weight: 4.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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** A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.072456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061315 restraints weight = 42957.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.062754 restraints weight = 25821.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063798 restraints weight = 18159.107| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9518 Z= 0.134 Angle : 0.681 9.010 12936 Z= 0.343 Chirality : 0.041 0.185 1474 Planarity : 0.006 0.074 1600 Dihedral : 4.986 22.328 1248 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.45 % Allowed : 9.84 % Favored : 86.71 % 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: -0.92 (0.26), residues: 1108 helix: 0.63 (0.19), residues: 794 sheet: -4.59 (0.77), residues: 20 loop : -3.85 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 706 HIS 0.003 0.001 HIS B 619 PHE 0.014 0.001 PHE A 616 TYR 0.011 0.001 TYR A 180 ARG 0.009 0.001 ARG A 425 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 570) hydrogen bonds : angle 4.29435 ( 1710) covalent geometry : bond 0.00269 ( 9518) covalent geometry : angle 0.68068 (12936) *********************** 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 97 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8372 (ttp) cc_final: 0.8069 (ttp) REVERT: B 232 GLU cc_start: 0.8628 (tp30) cc_final: 0.8424 (tp30) REVERT: B 335 MET cc_start: 0.8088 (mmm) cc_final: 0.7863 (mmt) REVERT: A 545 ARG cc_start: 0.8021 (mmp-170) cc_final: 0.6313 (ptp-170) REVERT: A 641 ARG cc_start: 0.8474 (ttt90) cc_final: 0.8228 (ptt90) outliers start: 34 outliers final: 11 residues processed: 95 average time/residue: 0.2084 time to fit residues: 28.6367 Evaluate side-chains 64 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 517 ILE Chi-restraints excluded: chain B residue 635 LEU 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 106 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.068658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.057483 restraints weight = 43733.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058781 restraints weight = 27027.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059695 restraints weight = 19364.485| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9518 Z= 0.247 Angle : 0.766 13.487 12936 Z= 0.391 Chirality : 0.045 0.198 1474 Planarity : 0.006 0.068 1600 Dihedral : 5.150 25.402 1248 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 2.54 % Allowed : 11.26 % Favored : 86.21 % 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: -0.43 (0.27), residues: 1108 helix: 0.96 (0.19), residues: 798 sheet: -4.37 (0.82), residues: 20 loop : -3.60 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 541 HIS 0.006 0.002 HIS A 130 PHE 0.020 0.002 PHE B 433 TYR 0.017 0.002 TYR A 506 ARG 0.007 0.001 ARG B 562 Details of bonding type rmsd hydrogen bonds : bond 0.05562 ( 570) hydrogen bonds : angle 4.49620 ( 1710) covalent geometry : bond 0.00544 ( 9518) covalent geometry : angle 0.76610 (12936) *********************** 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 75 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 1.127 Fit side-chains REVERT: B 192 MET cc_start: 0.8543 (ttp) cc_final: 0.8277 (ttp) REVERT: B 524 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8847 (mp) REVERT: A 340 LEU cc_start: 0.9123 (tt) cc_final: 0.8878 (mt) REVERT: A 641 ARG cc_start: 0.8596 (ttt90) cc_final: 0.8273 (ptt90) outliers start: 25 outliers final: 20 residues processed: 72 average time/residue: 0.2096 time to fit residues: 22.8079 Evaluate side-chains 68 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 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 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 A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 321 VAL 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 573 LEU Chi-restraints excluded: chain A residue 588 VAL 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 85 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** ** A 49 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 = 0.3385 r_free = 0.3385 target = 0.069421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058236 restraints weight = 43255.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059553 restraints weight = 26450.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060482 restraints weight = 19003.507| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9518 Z= 0.176 Angle : 0.688 9.288 12936 Z= 0.348 Chirality : 0.042 0.191 1474 Planarity : 0.005 0.064 1600 Dihedral : 4.936 22.797 1248 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 2.74 % Allowed : 12.07 % Favored : 85.19 % 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: -0.14 (0.27), residues: 1108 helix: 1.17 (0.19), residues: 796 sheet: -4.32 (0.81), residues: 20 loop : -3.47 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 541 HIS 0.004 0.001 HIS A 130 PHE 0.012 0.001 PHE B 433 TYR 0.012 0.001 TYR A 506 ARG 0.005 0.001 ARG B 89 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 570) hydrogen bonds : angle 4.30384 ( 1710) covalent geometry : bond 0.00387 ( 9518) covalent geometry : angle 0.68790 (12936) *********************** 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 79 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8545 (ttp) cc_final: 0.8243 (ttp) REVERT: B 515 MET cc_start: 0.8492 (tmm) cc_final: 0.8196 (tmm) REVERT: A 340 LEU cc_start: 0.9135 (tt) cc_final: 0.8864 (mt) REVERT: A 641 ARG cc_start: 0.8583 (ttt90) cc_final: 0.8317 (ptt90) outliers start: 27 outliers final: 21 residues processed: 75 average time/residue: 0.2140 time to fit residues: 24.0191 Evaluate side-chains 66 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 152 MET 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 525 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 335 MET 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 573 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 588 VAL 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 12 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 347 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058545 restraints weight = 43092.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.059880 restraints weight = 26391.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.060756 restraints weight = 18892.045| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9518 Z= 0.158 Angle : 0.662 8.476 12936 Z= 0.336 Chirality : 0.041 0.197 1474 Planarity : 0.005 0.063 1600 Dihedral : 4.748 22.473 1248 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.94 % Allowed : 12.47 % 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 (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: 0.08 (0.27), residues: 1108 helix: 1.35 (0.19), residues: 792 sheet: -4.26 (0.81), residues: 20 loop : -3.37 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 541 HIS 0.003 0.001 HIS B 130 PHE 0.012 0.001 PHE A 253 TYR 0.011 0.001 TYR A 506 ARG 0.006 0.001 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 570) hydrogen bonds : angle 4.20378 ( 1710) covalent geometry : bond 0.00346 ( 9518) covalent geometry : angle 0.66249 (12936) *********************** 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 81 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 1.006 Fit side-chains REVERT: B 192 MET cc_start: 0.8570 (ttp) cc_final: 0.8260 (ttp) REVERT: B 294 LEU cc_start: 0.9314 (tp) cc_final: 0.9109 (tt) REVERT: B 524 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8800 (mp) REVERT: B 545 ARG cc_start: 0.8095 (mmp-170) cc_final: 0.6687 (ptp-170) REVERT: A 152 MET cc_start: 0.8758 (tpt) cc_final: 0.8487 (ttp) REVERT: A 340 LEU cc_start: 0.9102 (tt) cc_final: 0.8826 (mt) REVERT: A 524 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8757 (mp) REVERT: A 545 ARG cc_start: 0.7970 (mmp-170) cc_final: 0.6528 (ptp-170) REVERT: A 641 ARG cc_start: 0.8572 (ttt90) cc_final: 0.8334 (ptt-90) outliers start: 29 outliers final: 24 residues processed: 76 average time/residue: 0.1960 time to fit residues: 21.8422 Evaluate side-chains 72 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 152 MET 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 380 LEU 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 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 587 LEU Chi-restraints excluded: chain A residue 588 VAL 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 53 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 347 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.067834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.056421 restraints weight = 43913.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.057686 restraints weight = 26625.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058524 restraints weight = 19156.628| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9518 Z= 0.228 Angle : 0.754 11.772 12936 Z= 0.382 Chirality : 0.044 0.217 1474 Planarity : 0.005 0.064 1600 Dihedral : 4.996 22.628 1248 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 2.94 % Allowed : 12.88 % Favored : 84.18 % 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: 0.08 (0.27), residues: 1108 helix: 1.31 (0.19), residues: 794 sheet: -4.26 (0.83), residues: 20 loop : -3.26 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 541 HIS 0.005 0.002 HIS A 130 PHE 0.015 0.002 PHE B 548 TYR 0.021 0.002 TYR A 506 ARG 0.006 0.001 ARG B 89 Details of bonding type rmsd hydrogen bonds : bond 0.05397 ( 570) hydrogen bonds : angle 4.44744 ( 1710) covalent geometry : bond 0.00508 ( 9518) covalent geometry : angle 0.75440 (12936) *********************** 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 74 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 45 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8640 (ttp) cc_final: 0.8353 (ttp) REVERT: B 524 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8844 (mp) REVERT: B 545 ARG cc_start: 0.8177 (mmp-170) cc_final: 0.6661 (ptp-170) REVERT: A 524 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8799 (mp) REVERT: A 545 ARG cc_start: 0.8053 (mmp-170) cc_final: 0.6656 (ptp-170) REVERT: A 641 ARG cc_start: 0.8710 (ttt90) cc_final: 0.8274 (ptt90) outliers start: 29 outliers final: 24 residues processed: 69 average time/residue: 0.2208 time to fit residues: 22.0822 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 : 1.050 ------------------------------------------------------------------------------- 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 152 MET Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 222 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 635 LEU 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 517 ILE 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 588 VAL 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 21 optimal weight: 0.0270 chunk 35 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.069897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058655 restraints weight = 43764.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060014 restraints weight = 26521.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060940 restraints weight = 18872.689| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9518 Z= 0.141 Angle : 0.673 10.049 12936 Z= 0.334 Chirality : 0.041 0.192 1474 Planarity : 0.005 0.061 1600 Dihedral : 4.672 20.875 1248 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.54 % Allowed : 13.39 % Favored : 84.08 % 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: 0.29 (0.27), residues: 1108 helix: 1.51 (0.19), residues: 792 sheet: -4.28 (0.80), residues: 20 loop : -3.29 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 541 HIS 0.003 0.001 HIS A 130 PHE 0.011 0.001 PHE A 616 TYR 0.009 0.001 TYR A 180 ARG 0.004 0.000 ARG B 562 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 570) hydrogen bonds : angle 4.15892 ( 1710) covalent geometry : bond 0.00301 ( 9518) covalent geometry : angle 0.67312 (12936) *********************** 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 73 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8512 (ttp) cc_final: 0.8229 (ttp) REVERT: B 524 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8786 (mp) REVERT: B 545 ARG cc_start: 0.8001 (mmp-170) cc_final: 0.6561 (ptp-170) REVERT: A 545 ARG cc_start: 0.7939 (mmp-170) cc_final: 0.6712 (ptp-170) outliers start: 25 outliers final: 19 residues processed: 70 average time/residue: 0.2007 time to fit residues: 20.9977 Evaluate side-chains 66 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 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 222 VAL 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 588 VAL 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 80 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 49 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 = 0.3395 r_free = 0.3395 target = 0.069911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058662 restraints weight = 43580.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059965 restraints weight = 26773.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060855 restraints weight = 19238.574| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9518 Z= 0.154 Angle : 0.675 11.082 12936 Z= 0.337 Chirality : 0.041 0.192 1474 Planarity : 0.005 0.062 1600 Dihedral : 4.635 21.272 1248 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % 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 (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: 0.39 (0.27), residues: 1108 helix: 1.59 (0.19), residues: 790 sheet: -4.23 (0.81), residues: 20 loop : -3.24 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 706 HIS 0.003 0.001 HIS A 130 PHE 0.010 0.001 PHE B 615 TYR 0.010 0.001 TYR A 506 ARG 0.004 0.000 ARG B 89 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 570) hydrogen bonds : angle 4.16172 ( 1710) covalent geometry : bond 0.00336 ( 9518) covalent geometry : angle 0.67498 (12936) *********************** 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 68 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8495 (ttp) cc_final: 0.8199 (ttp) REVERT: B 524 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8773 (mp) REVERT: B 545 ARG cc_start: 0.7947 (mmp-170) cc_final: 0.6557 (ptp-170) REVERT: A 545 ARG cc_start: 0.7960 (mmp-170) cc_final: 0.6764 (ptp-170) REVERT: A 641 ARG cc_start: 0.7247 (ptt-90) cc_final: 0.6666 (ptt-90) outliers start: 23 outliers final: 19 residues processed: 64 average time/residue: 0.2049 time to fit residues: 19.5020 Evaluate side-chains 63 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 635 LEU 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 222 VAL 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 587 LEU Chi-restraints excluded: chain A residue 588 VAL 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 22 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 0.0270 chunk 110 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 67 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 92 optimal weight: 0.0030 chunk 99 optimal weight: 0.9990 overall best weight: 0.3650 ------------------------------------------------------------------------------- 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** B 709 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.072228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061044 restraints weight = 43509.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062441 restraints weight = 26373.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.063399 restraints weight = 18743.391| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9518 Z= 0.122 Angle : 0.639 9.061 12936 Z= 0.316 Chirality : 0.040 0.192 1474 Planarity : 0.005 0.061 1600 Dihedral : 4.362 19.339 1248 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.83 % Allowed : 13.89 % 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 (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: 0.50 (0.27), residues: 1108 helix: 1.70 (0.19), residues: 790 sheet: -4.10 (0.80), residues: 20 loop : -3.30 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 706 HIS 0.004 0.001 HIS B 619 PHE 0.011 0.001 PHE B 549 TYR 0.007 0.001 TYR A 180 ARG 0.003 0.000 ARG B 89 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 570) hydrogen bonds : angle 3.96421 ( 1710) covalent geometry : bond 0.00243 ( 9518) covalent geometry : angle 0.63880 (12936) ********************** 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 77 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8535 (ttp) cc_final: 0.8225 (ttp) REVERT: B 282 LEU cc_start: 0.7651 (tp) cc_final: 0.6509 (mt) REVERT: B 524 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8772 (mp) REVERT: B 545 ARG cc_start: 0.7713 (mmp-170) cc_final: 0.6543 (ptp-170) REVERT: A 545 ARG cc_start: 0.7741 (mmp-170) cc_final: 0.6692 (ptp-170) REVERT: A 641 ARG cc_start: 0.6693 (ptt-90) cc_final: 0.6234 (ptt-90) outliers start: 18 outliers final: 13 residues processed: 76 average time/residue: 0.2035 time to fit residues: 22.9433 Evaluate side-chains 61 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 635 LEU 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 222 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.071126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060024 restraints weight = 42980.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061390 restraints weight = 26028.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062311 restraints weight = 18527.858| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9518 Z= 0.137 Angle : 0.661 9.239 12936 Z= 0.325 Chirality : 0.041 0.194 1474 Planarity : 0.005 0.061 1600 Dihedral : 4.315 19.776 1248 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.62 % Allowed : 14.50 % Favored : 83.87 % 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: 0.61 (0.27), residues: 1108 helix: 1.75 (0.19), residues: 790 sheet: -3.63 (0.90), residues: 20 loop : -3.18 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 706 HIS 0.003 0.001 HIS A 130 PHE 0.029 0.001 PHE A 383 TYR 0.008 0.001 TYR A 180 ARG 0.004 0.000 ARG B 562 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 570) hydrogen bonds : angle 3.94586 ( 1710) covalent geometry : bond 0.00302 ( 9518) covalent geometry : angle 0.66119 (12936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2491.83 seconds wall clock time: 44 minutes 11.71 seconds (2651.71 seconds total)