Starting phenix.real_space_refine on Thu Feb 13 19:55:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dz7_8931/02_2025/6dz7_8931.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dz7_8931/02_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_8931/02_2025/6dz7_8931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dz7_8931/02_2025/6dz7_8931.map" model { file = "/net/cci-nas-00/data/ceres_data/6dz7_8931/02_2025/6dz7_8931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dz7_8931/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 8.63, per 1000 atoms: 0.93 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: 2.12 Conformation dependent library (CDL) restraints added in 1.2 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: 0.75 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: 2.44 Time building geometry restraints manager: 2.49 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.340 Find NCS groups from input model: 0.160 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- 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= 0.609 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 *********************** 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 : 1.047 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: 0.2974 time to fit residues: 46.0563 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 = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060330 restraints weight = 42323.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061719 restraints weight = 25931.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062712 restraints weight = 18514.863| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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= 0.208 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 *********************** 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 : 1.127 Fit side-chains REVERT: B 286 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8055 (t80) REVERT: B 335 MET cc_start: 0.8049 (mmm) cc_final: 0.7838 (mmt) REVERT: B 514 GLU cc_start: 0.8243 (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: 0.8465 (ttt90) cc_final: 0.8261 (ptt-90) REVERT: A 641 ARG cc_start: 0.8649 (ttt90) cc_final: 0.7943 (ptt90) outliers start: 19 outliers final: 7 residues processed: 88 average time/residue: 0.2388 time to fit residues: 29.5289 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 : 1.121 ------------------------------------------------------------------------------- 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: 0.6980 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- 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 ** 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 = 0.3407 r_free = 0.3407 target = 0.070450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059205 restraints weight = 43468.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060553 restraints weight = 26552.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061536 restraints weight = 18817.754| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9518 Z= 0.235 Angle : 0.716 8.454 12936 Z= 0.365 Chirality : 0.043 0.198 1474 Planarity : 0.006 0.076 1600 Dihedral : 5.219 23.934 1248 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.25 % Allowed : 9.63 % Favored : 87.12 % 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: -0.94 (0.26), residues: 1108 helix: 0.59 (0.19), residues: 796 sheet: -4.72 (0.78), residues: 20 loop : -3.79 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 706 HIS 0.004 0.001 HIS A 130 PHE 0.013 0.001 PHE A 616 TYR 0.012 0.001 TYR A 180 ARG 0.009 0.001 ARG A 425 *********************** 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 90 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 1.046 Fit side-chains REVERT: B 192 MET cc_start: 0.8479 (ttp) cc_final: 0.8233 (ttp) REVERT: B 335 MET cc_start: 0.8221 (mmm) cc_final: 0.8013 (mmt) REVERT: A 152 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8185 (tpt) REVERT: A 294 LEU cc_start: 0.9414 (tp) cc_final: 0.9204 (tt) REVERT: A 340 LEU cc_start: 0.9127 (tt) cc_final: 0.8893 (mt) REVERT: A 641 ARG cc_start: 0.8542 (ttt90) cc_final: 0.8196 (ptt90) outliers start: 32 outliers final: 12 residues processed: 87 average time/residue: 0.2050 time to fit residues: 26.1103 Evaluate side-chains 64 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 152 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.069943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058714 restraints weight = 43548.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060045 restraints weight = 26884.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060967 restraints weight = 19250.226| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2933 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= 0.236 Angle : 0.687 7.552 12936 Z= 0.351 Chirality : 0.042 0.190 1474 Planarity : 0.005 0.066 1600 Dihedral : 5.011 24.129 1248 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 2.33 % Allowed : 10.85 % 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 (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: -0.44 (0.27), residues: 1108 helix: 0.98 (0.19), residues: 794 sheet: -4.56 (0.77), residues: 20 loop : -3.64 (0.33), residues: 294 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 0.020 0.001 PHE B 433 TYR 0.010 0.001 TYR A 180 ARG 0.005 0.001 ARG A 425 *********************** 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 77 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8492 (ttp) cc_final: 0.8199 (ttp) REVERT: B 515 MET cc_start: 0.8428 (tmm) cc_final: 0.8204 (tmm) REVERT: A 340 LEU cc_start: 0.9116 (tt) cc_final: 0.8871 (mt) REVERT: A 641 ARG cc_start: 0.8518 (ttt90) cc_final: 0.8298 (ptt90) outliers start: 23 outliers final: 20 residues processed: 73 average time/residue: 0.2209 time to fit residues: 23.4850 Evaluate side-chains 68 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 130 HIS 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 587 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 85 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.070221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058994 restraints weight = 43313.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060345 restraints weight = 26652.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061287 restraints weight = 19055.973| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9518 Z= 0.214 Angle : 0.678 14.425 12936 Z= 0.339 Chirality : 0.041 0.191 1474 Planarity : 0.005 0.062 1600 Dihedral : 4.822 22.637 1248 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.33 % Allowed : 11.97 % Favored : 85.70 % 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: -0.20 (0.27), residues: 1108 helix: 1.16 (0.19), residues: 794 sheet: -4.49 (0.78), residues: 20 loop : -3.55 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 541 HIS 0.003 0.001 HIS A 130 PHE 0.013 0.001 PHE A 549 TYR 0.010 0.001 TYR A 506 ARG 0.008 0.001 ARG B 562 *********************** 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 74 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 1.147 Fit side-chains REVERT: B 192 MET cc_start: 0.8547 (ttp) cc_final: 0.8261 (ttp) REVERT: B 294 LEU cc_start: 0.9323 (tp) cc_final: 0.9114 (tt) REVERT: B 515 MET cc_start: 0.8462 (tmm) cc_final: 0.8161 (tmm) REVERT: B 524 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8724 (mp) REVERT: B 545 ARG cc_start: 0.8091 (mmp-170) cc_final: 0.7611 (mmm160) REVERT: A 340 LEU cc_start: 0.9124 (tt) cc_final: 0.8870 (mt) REVERT: A 545 ARG cc_start: 0.8008 (mmp-170) cc_final: 0.6540 (ptp-170) outliers start: 23 outliers final: 18 residues processed: 72 average time/residue: 0.2016 time to fit residues: 21.5284 Evaluate side-chains 68 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 117 VAL 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 573 LEU Chi-restraints excluded: chain A residue 587 LEU 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: 10.0000 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 171 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.068614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057357 restraints weight = 43611.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058635 restraints weight = 27020.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.059521 restraints weight = 19461.803| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3458 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= 0.289 Angle : 0.712 10.508 12936 Z= 0.363 Chirality : 0.043 0.191 1474 Planarity : 0.005 0.065 1600 Dihedral : 4.936 23.451 1248 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 3.25 % Allowed : 11.66 % Favored : 85.09 % 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: 1.21 (0.19), residues: 794 sheet: -4.45 (0.81), residues: 20 loop : -3.38 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 541 HIS 0.005 0.001 HIS B 130 PHE 0.014 0.002 PHE A 253 TYR 0.018 0.002 TYR A 506 ARG 0.008 0.001 ARG B 562 *********************** 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: 32 poor density : 49 time to evaluate : 1.186 Fit side-chains REVERT: B 192 MET cc_start: 0.8609 (ttp) cc_final: 0.8317 (ttp) REVERT: B 294 LEU cc_start: 0.9334 (tp) cc_final: 0.9126 (tt) REVERT: B 524 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8867 (mp) REVERT: A 152 MET cc_start: 0.8221 (tpt) cc_final: 0.7978 (ttt) REVERT: A 340 LEU cc_start: 0.9129 (tt) cc_final: 0.8866 (mt) REVERT: A 545 ARG cc_start: 0.8057 (mmp-170) cc_final: 0.6641 (ptp-170) outliers start: 32 outliers final: 24 residues processed: 79 average time/residue: 0.2088 time to fit residues: 24.0183 Evaluate side-chains 70 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 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 217 CYS 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 517 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 573 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 53 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.069547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058277 restraints weight = 43516.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059599 restraints weight = 26499.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060527 restraints weight = 18927.651| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9518 Z= 0.225 Angle : 0.687 11.207 12936 Z= 0.342 Chirality : 0.041 0.188 1474 Planarity : 0.005 0.064 1600 Dihedral : 4.769 23.273 1248 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % 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 (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: 0.09 (0.27), residues: 1108 helix: 1.36 (0.19), residues: 792 sheet: -4.45 (0.79), residues: 20 loop : -3.35 (0.35), residues: 296 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 0.011 0.001 PHE B 615 TYR 0.011 0.001 TYR A 506 ARG 0.005 0.001 ARG B 562 *********************** 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: 25 poor density : 46 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8603 (ttp) cc_final: 0.8307 (ttp) REVERT: B 524 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8783 (mp) REVERT: B 545 ARG cc_start: 0.8107 (mmp-170) cc_final: 0.6696 (ptp-170) REVERT: A 545 ARG cc_start: 0.8016 (mmp-170) cc_final: 0.6654 (ptp-170) outliers start: 25 outliers final: 22 residues processed: 69 average time/residue: 0.1996 time to fit residues: 20.4540 Evaluate side-chains 69 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 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 21 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058162 restraints weight = 44280.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059472 restraints weight = 27147.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060383 restraints weight = 19455.110| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9518 Z= 0.233 Angle : 0.685 11.710 12936 Z= 0.343 Chirality : 0.042 0.189 1474 Planarity : 0.005 0.060 1600 Dihedral : 4.710 22.822 1248 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 2.64 % Allowed : 12.78 % 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: 0.21 (0.27), residues: 1108 helix: 1.44 (0.19), residues: 792 sheet: -4.38 (0.79), residues: 20 loop : -3.28 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 541 HIS 0.004 0.001 HIS A 130 PHE 0.013 0.001 PHE B 548 TYR 0.012 0.001 TYR A 506 ARG 0.005 0.001 ARG B 562 *********************** 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 71 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: B 152 MET cc_start: 0.8529 (tpp) cc_final: 0.8240 (tpt) REVERT: B 192 MET cc_start: 0.8530 (ttp) cc_final: 0.8243 (ttp) REVERT: B 524 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8820 (mp) REVERT: B 545 ARG cc_start: 0.8021 (mmp-170) cc_final: 0.6563 (ptp-170) REVERT: A 545 ARG cc_start: 0.7915 (mmp-170) cc_final: 0.6631 (ptp-170) outliers start: 26 outliers final: 23 residues processed: 69 average time/residue: 0.1790 time to fit residues: 18.8814 Evaluate side-chains 69 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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 573 LEU Chi-restraints excluded: chain A residue 587 LEU 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: 3.9990 chunk 70 optimal weight: 7.9990 chunk 92 optimal weight: 0.1980 chunk 82 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.070416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059243 restraints weight = 43157.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060591 restraints weight = 26240.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061517 restraints weight = 18723.872| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3860 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= 0.191 Angle : 0.662 9.872 12936 Z= 0.329 Chirality : 0.040 0.195 1474 Planarity : 0.005 0.059 1600 Dihedral : 4.554 21.822 1248 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.13 % Allowed : 13.29 % 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: 0.33 (0.27), residues: 1108 helix: 1.53 (0.19), residues: 792 sheet: -4.33 (0.79), residues: 20 loop : -3.24 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 541 HIS 0.003 0.001 HIS A 130 PHE 0.010 0.001 PHE B 615 TYR 0.009 0.001 TYR A 180 ARG 0.005 0.000 ARG A 641 *********************** 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: 21 poor density : 48 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8511 (ttp) cc_final: 0.8209 (ttp) REVERT: B 524 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8791 (mp) REVERT: B 545 ARG cc_start: 0.7974 (mmp-170) cc_final: 0.6541 (ptp-170) REVERT: A 545 ARG cc_start: 0.7826 (mmp-170) cc_final: 0.6621 (ptp-170) outliers start: 21 outliers final: 18 residues processed: 67 average time/residue: 0.1928 time to fit residues: 19.8982 Evaluate side-chains 64 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP 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 553 VAL 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 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 22 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 99 optimal weight: 0.0670 overall best weight: 0.8922 ------------------------------------------------------------------------------- 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 ** 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 = 0.3424 r_free = 0.3424 target = 0.071202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059960 restraints weight = 43774.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.061315 restraints weight = 26671.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062140 restraints weight = 19051.724| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4026 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= 0.173 Angle : 0.654 10.755 12936 Z= 0.321 Chirality : 0.040 0.189 1474 Planarity : 0.005 0.059 1600 Dihedral : 4.387 21.981 1248 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.03 % Allowed : 13.89 % 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: 0.47 (0.27), residues: 1108 helix: 1.64 (0.19), residues: 792 sheet: -4.07 (0.82), residues: 20 loop : -3.23 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 227 HIS 0.003 0.001 HIS A 130 PHE 0.012 0.001 PHE B 549 TYR 0.009 0.001 TYR A 180 ARG 0.004 0.000 ARG B 562 ********************** 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 72 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8517 (ttp) cc_final: 0.8219 (ttp) REVERT: B 282 LEU cc_start: 0.7645 (tp) cc_final: 0.6497 (mt) REVERT: B 524 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8847 (mp) REVERT: B 545 ARG cc_start: 0.7894 (mmp-170) cc_final: 0.6519 (ptp-170) REVERT: A 545 ARG cc_start: 0.7820 (mmp-170) cc_final: 0.6666 (ptp-170) outliers start: 20 outliers final: 17 residues processed: 70 average time/residue: 0.1922 time to fit residues: 20.4713 Evaluate side-chains 65 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP 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 553 VAL Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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** ** 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 = 0.3386 r_free = 0.3386 target = 0.069511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058311 restraints weight = 43718.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059590 restraints weight = 26857.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060487 restraints weight = 19350.006| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4017 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= 0.268 Angle : 0.698 9.330 12936 Z= 0.350 Chirality : 0.042 0.200 1474 Planarity : 0.005 0.060 1600 Dihedral : 4.576 22.426 1248 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.23 % Allowed : 14.20 % Favored : 83.57 % 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: 0.53 (0.27), residues: 1108 helix: 1.67 (0.19), residues: 790 sheet: -3.90 (0.89), residues: 20 loop : -3.13 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 706 HIS 0.005 0.001 HIS A 130 PHE 0.012 0.001 PHE B 615 TYR 0.015 0.001 TYR A 506 ARG 0.005 0.001 ARG B 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.31 seconds wall clock time: 41 minutes 18.81 seconds (2478.81 seconds total)