Starting phenix.real_space_refine on Wed Aug 5 06:39:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfk_71603/08_2026/9pfk_71603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfk_71603/08_2026/9pfk_71603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pfk_71603/08_2026/9pfk_71603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfk_71603/08_2026/9pfk_71603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pfk_71603/08_2026/9pfk_71603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfk_71603/08_2026/9pfk_71603.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 5452 2.51 5 N 1446 2.21 5 O 1640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8566 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2395 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 279} Chain: "H" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1000 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "L" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 888 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 105} Chain: "B" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2395 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 279} Chain: "C" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1000 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 888 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 105} Time building chain proxies: 1.86, per 1000 atoms: 0.22 Number of scatterers: 8566 At special positions: 0 Unit cell: (126.875, 99.325, 81.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1640 8.00 N 1446 7.00 C 5452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 402.4 milliseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 14 sheets defined 5.0% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.651A pdb=" N ASN A 282 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 454 through 465 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.540A pdb=" N THR H 31 " --> pdb=" O PHE H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.651A pdb=" N ASN B 282 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 283' Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.540A pdb=" N THR C 31 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 505 through 506 removed outlier: 3.574A pdb=" N HIS A 505 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL A 497 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE A 487 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A 472 " --> pdb=" O TRP A 520 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TRP A 520 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU A 474 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 442 removed outlier: 7.368A pdb=" N CYS A 441 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL A 388 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN A 331 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 388 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LYS A 329 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR A 352 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLN A 366 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 286 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.222A pdb=" N TRP H 35A" --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.776A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP H 101 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR H 100F" --> pdb=" O TRP H 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.622A pdb=" N ILE L 75 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.811A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL L 13 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 505 through 506 removed outlier: 3.589A pdb=" N HIS B 505 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL B 497 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE B 487 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL B 472 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TRP B 520 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B 474 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 440 through 442 removed outlier: 7.367A pdb=" N CYS B 441 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL B 388 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN B 331 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL B 388 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS B 329 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TYR B 352 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLN B 366 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 286 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.223A pdb=" N TRP C 35A" --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS C 50 " --> pdb=" O TRP C 35A" (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 44 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.777A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP C 101 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR C 100F" --> pdb=" O TRP C 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.619A pdb=" N ILE D 75 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.811A pdb=" N ASP D 105 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL D 13 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP D 35 " --> pdb=" O ILE D 47 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.85 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: 2746 1.34 - 1.47: 2314 1.47 - 1.59: 3718 1.59 - 1.71: 0 1.71 - 1.84: 38 Bond restraints: 8816 Sorted by residual: bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.29e+00 bond pdb=" N GLN C 1 " pdb=" CA GLN C 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.26e+00 bond pdb=" CG1 ILE L 94 " pdb=" CD1 ILE L 94 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.92e+00 bond pdb=" N GLU L 1 " pdb=" CA GLU L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N GLU D 1 " pdb=" CA GLU D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 ... (remaining 8811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 10932 1.54 - 3.09: 855 3.09 - 4.63: 181 4.63 - 6.18: 55 6.18 - 7.72: 15 Bond angle restraints: 12038 Sorted by residual: angle pdb=" CA ASN L 29 " pdb=" CB ASN L 29 " pdb=" CG ASN L 29 " ideal model delta sigma weight residual 112.60 116.72 -4.12 1.00e+00 1.00e+00 1.70e+01 angle pdb=" CA ASN D 29 " pdb=" CB ASN D 29 " pdb=" CG ASN D 29 " ideal model delta sigma weight residual 112.60 116.60 -4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" CA TYR A 444 " pdb=" CB TYR A 444 " pdb=" CG TYR A 444 " ideal model delta sigma weight residual 113.90 120.78 -6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" CA TYR B 444 " pdb=" CB TYR B 444 " pdb=" CG TYR B 444 " ideal model delta sigma weight residual 113.90 120.78 -6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" CA TYR H 100F" pdb=" CB TYR H 100F" pdb=" CG TYR H 100F" ideal model delta sigma weight residual 113.90 120.71 -6.81 1.80e+00 3.09e-01 1.43e+01 ... (remaining 12033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 4761 17.48 - 34.96: 287 34.96 - 52.44: 70 52.44 - 69.92: 28 69.92 - 87.40: 8 Dihedral angle restraints: 5154 sinusoidal: 2018 harmonic: 3136 Sorted by residual: dihedral pdb=" CD ARG B 373 " pdb=" NE ARG B 373 " pdb=" CZ ARG B 373 " pdb=" NH1 ARG B 373 " ideal model delta sinusoidal sigma weight residual 0.00 -80.36 80.36 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CD ARG A 373 " pdb=" NE ARG A 373 " pdb=" CZ ARG A 373 " pdb=" NH1 ARG A 373 " ideal model delta sinusoidal sigma weight residual 0.00 -80.27 80.27 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CD ARG B 297 " pdb=" NE ARG B 297 " pdb=" CZ ARG B 297 " pdb=" NH1 ARG B 297 " ideal model delta sinusoidal sigma weight residual 0.00 -66.20 66.20 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 5151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 965 0.057 - 0.115: 285 0.115 - 0.172: 44 0.172 - 0.229: 6 0.229 - 0.286: 2 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA ILE L 94 " pdb=" N ILE L 94 " pdb=" C ILE L 94 " pdb=" CB ILE L 94 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ILE D 94 " pdb=" N ILE D 94 " pdb=" C ILE D 94 " pdb=" CB ILE D 94 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA PHE C 100G" pdb=" N PHE C 100G" pdb=" C PHE C 100G" pdb=" CB PHE C 100G" both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1299 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 373 " -0.953 9.50e-02 1.11e+02 4.28e-01 1.18e+02 pdb=" NE ARG B 373 " 0.075 2.00e-02 2.50e+03 pdb=" CZ ARG B 373 " -0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG B 373 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 373 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 373 " 0.953 9.50e-02 1.11e+02 4.28e-01 1.18e+02 pdb=" NE ARG A 373 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 373 " 0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG A 373 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 373 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 297 " -0.858 9.50e-02 1.11e+02 3.85e-01 9.82e+01 pdb=" NE ARG B 297 " 0.070 2.00e-02 2.50e+03 pdb=" CZ ARG B 297 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG B 297 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 297 " -0.006 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 107 2.62 - 3.19: 7408 3.19 - 3.76: 12896 3.76 - 4.33: 18384 4.33 - 4.90: 31702 Nonbonded interactions: 70497 Sorted by model distance: nonbonded pdb=" O TYR D 49 " pdb=" OH TYR D 91 " model vdw 2.053 3.040 nonbonded pdb=" O TYR L 49 " pdb=" OH TYR L 91 " model vdw 2.056 3.040 nonbonded pdb=" OD1 ASN A 446 " pdb=" OG SER H 100 " model vdw 2.085 3.040 nonbonded pdb=" OD1 ASN B 446 " pdb=" OG SER C 100 " model vdw 2.086 3.040 nonbonded pdb=" OH TYR A 299 " pdb=" O ASP A 372 " model vdw 2.132 3.040 ... (remaining 70492 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'C' } ncs_group { reference = chain 'L' selection = chain 'D' } 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 individual isotropic 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: 5.280 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.240 Find NCS groups from input model: 0.040 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:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.006 0.067 8820 Z= 0.238 Angle : 0.999 7.720 12046 Z= 0.546 Chirality : 0.055 0.286 1302 Planarity : 0.042 0.428 1572 Dihedral : 13.318 87.404 3142 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.59 % Allowed : 1.90 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.24), residues: 1076 helix: 0.98 (1.11), residues: 22 sheet: -0.10 (0.28), residues: 338 loop : 0.18 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.015 ARG H 94 TYR 0.035 0.003 TYR L 91 PHE 0.039 0.003 PHE B 461 TRP 0.012 0.002 TRP A 520 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 ( 8816) covalent geometry : angle 0.99831 / 0.55 (12038) SS BOND : bond 0.00376 / 0.18 ( 4) SS BOND : angle 2.03295 / 0.94 ( 8) hydrogen bonds : bond 0.25146 / 16.51 ( 240) hydrogen bonds : angle 11.51309 / 8.00 ( 642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 0.375 Fit side-chains REVERT: A 316 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7643 (pp20) REVERT: A 348 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8603 (pptt) REVERT: A 505 HIS cc_start: 0.8113 (t70) cc_final: 0.7688 (t70) REVERT: L 28 ASN cc_start: 0.7751 (p0) cc_final: 0.7534 (p0) REVERT: B 316 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7646 (pp20) REVERT: B 348 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8604 (pptt) REVERT: B 505 HIS cc_start: 0.8092 (t70) cc_final: 0.7677 (t70) outliers start: 15 outliers final: 8 residues processed: 251 average time/residue: 0.5601 time to fit residues: 149.8058 Evaluate side-chains 171 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain D residue 91 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN A 378 ASN A 380 ASN A 430 GLN A 505 HIS H 77 GLN L 37 GLN L 79 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 378 ASN B 380 ASN B 430 GLN B 446 ASN C 77 GLN D 37 GLN D 79 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.157503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.140911 restraints weight = 15118.621| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 3.39 r_work: 0.4319 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8820 Z= 0.174 Angle : 0.711 6.685 12046 Z= 0.385 Chirality : 0.049 0.177 1302 Planarity : 0.006 0.062 1572 Dihedral : 6.942 55.637 1214 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.59 % Allowed : 11.21 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1076 helix: 1.02 (1.21), residues: 24 sheet: -0.38 (0.26), residues: 378 loop : 0.60 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 484 TYR 0.020 0.002 TYR A 311 PHE 0.013 0.002 PHE A 517 TRP 0.012 0.001 TRP A 520 HIS 0.006 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 8816) covalent geometry : angle 0.71076 / 0.38 (12038) SS BOND : bond 0.00464 / 0.23 ( 4) SS BOND : angle 1.05165 / 0.49 ( 8) hydrogen bonds : bond 0.04265 / 2.73 ( 240) hydrogen bonds : angle 7.82312 / 5.44 ( 642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7710 (pp20) cc_final: 0.7487 (pp20) REVERT: A 348 LYS cc_start: 0.8944 (ptmt) cc_final: 0.8270 (pptt) REVERT: A 438 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8168 (mpt) REVERT: H 13 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8901 (mmtt) REVERT: H 46 GLU cc_start: 0.8416 (tt0) cc_final: 0.8128 (tt0) REVERT: B 247 GLU cc_start: 0.7699 (pp20) cc_final: 0.7478 (pp20) REVERT: B 348 LYS cc_start: 0.8938 (ptmt) cc_final: 0.8266 (pptt) REVERT: B 401 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: B 438 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8177 (mpt) REVERT: C 46 GLU cc_start: 0.8399 (tt0) cc_final: 0.8108 (tt0) outliers start: 34 outliers final: 10 residues processed: 196 average time/residue: 0.5134 time to fit residues: 107.9568 Evaluate side-chains 165 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain C residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 0.0270 chunk 83 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 459 GLN A 504 GLN ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 378 ASN B 459 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.156169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.139238 restraints weight = 15097.489| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 3.42 r_work: 0.4297 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8820 Z= 0.147 Angle : 0.635 7.395 12046 Z= 0.339 Chirality : 0.046 0.167 1302 Planarity : 0.005 0.052 1572 Dihedral : 5.709 58.824 1194 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.28 % Allowed : 15.54 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1076 helix: 1.11 (1.19), residues: 24 sheet: -0.22 (0.26), residues: 374 loop : 0.62 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 364 TYR 0.024 0.002 TYR C 35 PHE 0.019 0.002 PHE A 426 TRP 0.010 0.001 TRP A 520 HIS 0.003 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 8816) covalent geometry : angle 0.63471 / 0.34 (12038) SS BOND : bond 0.00423 / 0.21 ( 4) SS BOND : angle 0.85332 / 0.41 ( 8) hydrogen bonds : bond 0.03683 / 2.36 ( 240) hydrogen bonds : angle 6.96965 / 4.85 ( 642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7693 (pp20) cc_final: 0.7338 (pp20) REVERT: A 348 LYS cc_start: 0.8940 (ptmt) cc_final: 0.8244 (pptt) REVERT: A 373 ARG cc_start: 0.8370 (ptp90) cc_final: 0.8056 (ptp90) REVERT: H 13 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8838 (mmtt) REVERT: H 46 GLU cc_start: 0.8468 (tt0) cc_final: 0.8114 (tt0) REVERT: H 72 ASP cc_start: 0.7521 (t0) cc_final: 0.6922 (m-30) REVERT: B 247 GLU cc_start: 0.7677 (pp20) cc_final: 0.7272 (pp20) REVERT: B 348 LYS cc_start: 0.8943 (ptmt) cc_final: 0.8250 (pptt) REVERT: B 373 ARG cc_start: 0.8359 (ptp90) cc_final: 0.8045 (ptp90) REVERT: C 46 GLU cc_start: 0.8458 (tt0) cc_final: 0.8116 (tt0) outliers start: 31 outliers final: 13 residues processed: 188 average time/residue: 0.4680 time to fit residues: 95.0923 Evaluate side-chains 164 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 31 optimal weight: 0.0980 chunk 96 optimal weight: 3.9990 chunk 91 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN A 309 ASN A 366 GLN A 378 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.151621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.134327 restraints weight = 15204.336| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 3.44 r_work: 0.4214 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8820 Z= 0.186 Angle : 0.643 6.756 12046 Z= 0.342 Chirality : 0.047 0.165 1302 Planarity : 0.005 0.042 1572 Dihedral : 4.938 21.595 1188 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.23 % Allowed : 15.75 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1076 helix: 1.13 (1.14), residues: 24 sheet: -0.24 (0.26), residues: 366 loop : 0.42 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 364 TYR 0.018 0.002 TYR H 35 PHE 0.014 0.002 PHE H 58 TRP 0.011 0.001 TRP L 50 HIS 0.002 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 8816) covalent geometry : angle 0.64314 / 0.34 (12038) SS BOND : bond 0.00477 / 0.24 ( 4) SS BOND : angle 0.94274 / 0.45 ( 8) hydrogen bonds : bond 0.03569 / 2.31 ( 240) hydrogen bonds : angle 6.85937 / 4.77 ( 642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.396 Fit side-chains REVERT: A 247 GLU cc_start: 0.7826 (pp20) cc_final: 0.7509 (pp20) REVERT: A 348 LYS cc_start: 0.8974 (ptmt) cc_final: 0.8232 (pptt) REVERT: A 401 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: H 13 LYS cc_start: 0.9085 (mmmm) cc_final: 0.8720 (mmtt) REVERT: H 15 SER cc_start: 0.8707 (m) cc_final: 0.8469 (t) REVERT: H 46 GLU cc_start: 0.8549 (tt0) cc_final: 0.8176 (tt0) REVERT: H 63 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7616 (pp) REVERT: L 79 GLN cc_start: 0.8159 (mt0) cc_final: 0.7957 (mt0) REVERT: B 247 GLU cc_start: 0.7796 (pp20) cc_final: 0.7563 (pp20) REVERT: B 348 LYS cc_start: 0.8967 (ptmt) cc_final: 0.8222 (pptt) REVERT: C 46 GLU cc_start: 0.8542 (tt0) cc_final: 0.8163 (tt0) REVERT: C 63 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7615 (pp) REVERT: D 79 GLN cc_start: 0.8159 (mt0) cc_final: 0.7955 (mt0) outliers start: 40 outliers final: 10 residues processed: 184 average time/residue: 0.4920 time to fit residues: 96.9944 Evaluate side-chains 165 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 98 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 366 GLN B 378 ASN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.152591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.135444 restraints weight = 15249.180| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 3.45 r_work: 0.4232 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8820 Z= 0.152 Angle : 0.621 7.114 12046 Z= 0.327 Chirality : 0.046 0.159 1302 Planarity : 0.005 0.039 1572 Dihedral : 4.857 20.545 1188 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.96 % Allowed : 18.50 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1076 helix: 1.46 (1.14), residues: 24 sheet: -0.26 (0.27), residues: 368 loop : 0.43 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 364 TYR 0.018 0.001 TYR C 35 PHE 0.012 0.001 PHE A 426 TRP 0.010 0.001 TRP A 520 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 8816) covalent geometry : angle 0.62097 / 0.33 (12038) SS BOND : bond 0.00324 / 0.16 ( 4) SS BOND : angle 0.72442 / 0.35 ( 8) hydrogen bonds : bond 0.03303 / 2.12 ( 240) hydrogen bonds : angle 6.61522 / 4.59 ( 642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.499 Fit side-chains REVERT: A 339 ARG cc_start: 0.7720 (mmp-170) cc_final: 0.7459 (mmm160) REVERT: A 348 LYS cc_start: 0.8999 (ptmt) cc_final: 0.8239 (pptt) REVERT: A 373 ARG cc_start: 0.8577 (ptp-110) cc_final: 0.8183 (ptp90) REVERT: A 401 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: H 13 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8709 (mmtt) REVERT: H 15 SER cc_start: 0.8704 (m) cc_final: 0.8476 (t) REVERT: H 46 GLU cc_start: 0.8589 (tt0) cc_final: 0.8207 (tt0) REVERT: H 63 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7716 (pp) REVERT: L 55 GLU cc_start: 0.7483 (tp30) cc_final: 0.6893 (tt0) REVERT: B 339 ARG cc_start: 0.7723 (mmp-170) cc_final: 0.7463 (mmm160) REVERT: B 348 LYS cc_start: 0.8981 (ptmt) cc_final: 0.8223 (pptt) REVERT: B 373 ARG cc_start: 0.8572 (ptp-110) cc_final: 0.8179 (ptp90) REVERT: C 15 SER cc_start: 0.8704 (m) cc_final: 0.8488 (t) REVERT: C 46 GLU cc_start: 0.8583 (tt0) cc_final: 0.8197 (tt0) REVERT: C 63 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7744 (pp) REVERT: D 55 GLU cc_start: 0.7456 (tp30) cc_final: 0.6861 (tt0) outliers start: 28 outliers final: 11 residues processed: 175 average time/residue: 0.4084 time to fit residues: 77.3209 Evaluate side-chains 163 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 0.0170 chunk 90 optimal weight: 0.0030 overall best weight: 0.4030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 ASN A 331 GLN A 378 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 331 GLN B 378 ASN B 446 ASN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.154507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.137698 restraints weight = 14998.472| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.41 r_work: 0.4263 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8820 Z= 0.127 Angle : 0.607 7.798 12046 Z= 0.318 Chirality : 0.046 0.152 1302 Planarity : 0.004 0.034 1572 Dihedral : 4.716 19.946 1188 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.75 % Allowed : 19.13 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1076 helix: 1.88 (1.14), residues: 24 sheet: -0.20 (0.27), residues: 368 loop : 0.42 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 364 TYR 0.017 0.001 TYR C 35 PHE 0.008 0.001 PHE C 78 TRP 0.009 0.001 TRP A 520 HIS 0.002 0.000 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8816) covalent geometry : angle 0.60712 / 0.32 (12038) SS BOND : bond 0.00201 / 0.10 ( 4) SS BOND : angle 0.53074 / 0.25 ( 8) hydrogen bonds : bond 0.03132 / 2.01 ( 240) hydrogen bonds : angle 6.34478 / 4.40 ( 642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 ARG cc_start: 0.7791 (mmp-170) cc_final: 0.7522 (mmm160) REVERT: A 348 LYS cc_start: 0.8969 (ptmt) cc_final: 0.8197 (pptt) REVERT: H 13 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8699 (mmtt) REVERT: H 15 SER cc_start: 0.8704 (m) cc_final: 0.8472 (t) REVERT: H 46 GLU cc_start: 0.8574 (tt0) cc_final: 0.8183 (tt0) REVERT: H 63 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7697 (pp) REVERT: L 55 GLU cc_start: 0.7477 (tp30) cc_final: 0.6874 (tt0) REVERT: B 339 ARG cc_start: 0.7794 (mmp-170) cc_final: 0.7526 (mmm160) REVERT: B 348 LYS cc_start: 0.8958 (ptmt) cc_final: 0.8182 (pptt) REVERT: C 15 SER cc_start: 0.8696 (m) cc_final: 0.8483 (t) REVERT: C 46 GLU cc_start: 0.8565 (tt0) cc_final: 0.8190 (tt0) REVERT: C 63 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7717 (pp) REVERT: D 55 GLU cc_start: 0.7473 (tp30) cc_final: 0.6854 (tt0) outliers start: 26 outliers final: 10 residues processed: 168 average time/residue: 0.3924 time to fit residues: 71.7123 Evaluate side-chains 153 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** D 28 ASN ** 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 = 0.4615 r_free = 0.4615 target = 0.153299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.136624 restraints weight = 15228.604| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 3.36 r_work: 0.4262 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8820 Z= 0.142 Angle : 0.622 8.228 12046 Z= 0.324 Chirality : 0.046 0.150 1302 Planarity : 0.005 0.044 1572 Dihedral : 4.692 19.706 1188 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.64 % Allowed : 20.51 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.25), residues: 1076 helix: 1.97 (1.13), residues: 24 sheet: -0.16 (0.26), residues: 368 loop : 0.37 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 364 TYR 0.016 0.001 TYR H 35 PHE 0.009 0.001 PHE B 426 TRP 0.008 0.001 TRP A 520 HIS 0.001 0.000 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 8816) covalent geometry : angle 0.62215 / 0.32 (12038) SS BOND : bond 0.00275 / 0.14 ( 4) SS BOND : angle 0.63426 / 0.30 ( 8) hydrogen bonds : bond 0.03084 / 1.98 ( 240) hydrogen bonds : angle 6.29263 / 4.36 ( 642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 348 LYS cc_start: 0.9057 (ptmt) cc_final: 0.8347 (pptt) REVERT: A 373 ARG cc_start: 0.8510 (ptp-110) cc_final: 0.8099 (ptp90) REVERT: H 13 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8774 (mmtt) REVERT: H 15 SER cc_start: 0.8776 (m) cc_final: 0.8515 (t) REVERT: H 46 GLU cc_start: 0.8537 (tt0) cc_final: 0.8241 (tt0) REVERT: H 63 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7846 (pp) REVERT: H 66 ARG cc_start: 0.8489 (ptt-90) cc_final: 0.8209 (ptt-90) REVERT: B 348 LYS cc_start: 0.9043 (ptmt) cc_final: 0.8335 (pptt) REVERT: B 373 ARG cc_start: 0.8503 (ptp-110) cc_final: 0.8091 (ptp90) REVERT: C 15 SER cc_start: 0.8759 (m) cc_final: 0.8514 (t) REVERT: C 46 GLU cc_start: 0.8517 (tt0) cc_final: 0.8217 (tt0) REVERT: C 63 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7853 (pp) REVERT: C 66 ARG cc_start: 0.8502 (ptt-90) cc_final: 0.8224 (ptt-90) outliers start: 25 outliers final: 10 residues processed: 170 average time/residue: 0.3889 time to fit residues: 71.8883 Evaluate side-chains 158 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 0.0170 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** D 28 ASN ** 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 = 0.4548 r_free = 0.4548 target = 0.148440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.131836 restraints weight = 15001.977| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 3.32 r_work: 0.4190 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8820 Z= 0.192 Angle : 0.671 8.722 12046 Z= 0.351 Chirality : 0.048 0.170 1302 Planarity : 0.005 0.051 1572 Dihedral : 4.933 20.413 1188 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.85 % Allowed : 20.82 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.25), residues: 1076 helix: 1.56 (1.09), residues: 24 sheet: -0.25 (0.26), residues: 370 loop : 0.33 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 364 TYR 0.014 0.002 TYR C 35 PHE 0.013 0.002 PHE C 97 TRP 0.013 0.002 TRP L 50 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 8816) covalent geometry : angle 0.67125 / 0.35 (12038) SS BOND : bond 0.00452 / 0.23 ( 4) SS BOND : angle 0.88583 / 0.42 ( 8) hydrogen bonds : bond 0.03319 / 2.15 ( 240) hydrogen bonds : angle 6.57483 / 4.57 ( 642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ARG cc_start: 0.7781 (mmp-170) cc_final: 0.7488 (mmm160) REVERT: A 348 LYS cc_start: 0.9072 (ptmt) cc_final: 0.8341 (pptt) REVERT: H 13 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8723 (mmpt) REVERT: H 15 SER cc_start: 0.8730 (m) cc_final: 0.8495 (t) REVERT: H 46 GLU cc_start: 0.8585 (tt0) cc_final: 0.8241 (tt0) REVERT: H 63 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7841 (pp) REVERT: L 55 GLU cc_start: 0.7412 (tp30) cc_final: 0.6964 (tt0) REVERT: B 339 ARG cc_start: 0.7772 (mmp-170) cc_final: 0.7478 (mmm160) REVERT: B 348 LYS cc_start: 0.9069 (ptmt) cc_final: 0.8340 (pptt) REVERT: C 15 SER cc_start: 0.8732 (m) cc_final: 0.8486 (t) REVERT: C 46 GLU cc_start: 0.8575 (tt0) cc_final: 0.8226 (tt0) REVERT: C 63 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7828 (pp) REVERT: C 66 ARG cc_start: 0.8502 (ptt-90) cc_final: 0.8229 (ptt-90) REVERT: D 55 GLU cc_start: 0.7402 (tp30) cc_final: 0.6965 (tt0) outliers start: 27 outliers final: 12 residues processed: 161 average time/residue: 0.4174 time to fit residues: 73.1869 Evaluate side-chains 154 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 ASN A 378 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 378 ASN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.151319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.134802 restraints weight = 15101.536| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 3.34 r_work: 0.4235 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8820 Z= 0.147 Angle : 0.641 9.309 12046 Z= 0.332 Chirality : 0.046 0.167 1302 Planarity : 0.004 0.045 1572 Dihedral : 4.771 19.754 1188 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.54 % Allowed : 21.99 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1076 helix: 1.94 (1.11), residues: 24 sheet: -0.26 (0.27), residues: 366 loop : 0.37 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 364 TYR 0.014 0.001 TYR H 35 PHE 0.008 0.001 PHE B 426 TRP 0.009 0.001 TRP B 308 HIS 0.002 0.000 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8816) covalent geometry : angle 0.64080 / 0.33 (12038) SS BOND : bond 0.00267 / 0.14 ( 4) SS BOND : angle 0.63141 / 0.30 ( 8) hydrogen bonds : bond 0.03069 / 1.96 ( 240) hydrogen bonds : angle 6.29509 / 4.37 ( 642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.337 Fit side-chains REVERT: A 348 LYS cc_start: 0.9037 (ptmt) cc_final: 0.8285 (pptt) REVERT: A 373 ARG cc_start: 0.8592 (ptp-110) cc_final: 0.8200 (ptp90) REVERT: H 13 LYS cc_start: 0.9095 (mmmm) cc_final: 0.8733 (mmtt) REVERT: H 15 SER cc_start: 0.8719 (m) cc_final: 0.8463 (t) REVERT: H 46 GLU cc_start: 0.8611 (tt0) cc_final: 0.8279 (tt0) REVERT: H 63 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7791 (pp) REVERT: H 66 ARG cc_start: 0.8460 (ptt-90) cc_final: 0.8203 (ptt-90) REVERT: L 55 GLU cc_start: 0.7353 (tp30) cc_final: 0.6929 (tt0) REVERT: B 348 LYS cc_start: 0.9028 (ptmt) cc_final: 0.8276 (pptt) REVERT: B 373 ARG cc_start: 0.8558 (ptp-110) cc_final: 0.8201 (ptp90) REVERT: C 15 SER cc_start: 0.8688 (m) cc_final: 0.8467 (t) REVERT: C 46 GLU cc_start: 0.8605 (tt0) cc_final: 0.8242 (tt0) REVERT: C 63 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7804 (pp) REVERT: C 66 ARG cc_start: 0.8491 (ptt-90) cc_final: 0.8212 (ptt-90) REVERT: D 55 GLU cc_start: 0.7350 (tp30) cc_final: 0.6920 (tt0) outliers start: 24 outliers final: 12 residues processed: 164 average time/residue: 0.4050 time to fit residues: 72.1700 Evaluate side-chains 151 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN A 378 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 378 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.149516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.133100 restraints weight = 14960.901| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 3.30 r_work: 0.4207 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8820 Z= 0.184 Angle : 0.672 9.487 12046 Z= 0.347 Chirality : 0.049 0.399 1302 Planarity : 0.005 0.058 1572 Dihedral : 4.890 20.023 1188 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.43 % Allowed : 22.73 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.25), residues: 1076 helix: 1.87 (1.11), residues: 24 sheet: -0.27 (0.27), residues: 366 loop : 0.32 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 364 TYR 0.014 0.002 TYR C 59 PHE 0.011 0.002 PHE C 97 TRP 0.025 0.002 TRP B 308 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 8816) covalent geometry : angle 0.67234 / 0.35 (12038) SS BOND : bond 0.00295 / 0.15 ( 4) SS BOND : angle 0.85622 / 0.41 ( 8) hydrogen bonds : bond 0.03126 / 2.02 ( 240) hydrogen bonds : angle 6.42833 / 4.47 ( 642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.260 Fit side-chains REVERT: A 348 LYS cc_start: 0.9070 (ptmt) cc_final: 0.8337 (pptt) REVERT: H 13 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8743 (mmpt) REVERT: H 15 SER cc_start: 0.8705 (m) cc_final: 0.8440 (t) REVERT: H 46 GLU cc_start: 0.8602 (tt0) cc_final: 0.8274 (tt0) REVERT: H 63 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7844 (pp) REVERT: H 66 ARG cc_start: 0.8512 (ptt-90) cc_final: 0.8264 (ptt-90) REVERT: L 55 GLU cc_start: 0.7427 (tp30) cc_final: 0.6995 (tt0) REVERT: B 348 LYS cc_start: 0.9063 (ptmt) cc_final: 0.8330 (pptt) REVERT: B 373 ARG cc_start: 0.8534 (ptp-110) cc_final: 0.8155 (ptp90) REVERT: C 15 SER cc_start: 0.8729 (m) cc_final: 0.8478 (t) REVERT: C 46 GLU cc_start: 0.8601 (tt0) cc_final: 0.8275 (tt0) REVERT: C 63 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7860 (pp) REVERT: C 66 ARG cc_start: 0.8515 (ptt-90) cc_final: 0.8250 (ptt-90) REVERT: D 55 GLU cc_start: 0.7395 (tp30) cc_final: 0.6979 (tt0) outliers start: 23 outliers final: 9 residues processed: 153 average time/residue: 0.3432 time to fit residues: 57.1548 Evaluate side-chains 146 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN A 378 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 378 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.150468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.133937 restraints weight = 15011.817| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 3.33 r_work: 0.4220 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8820 Z= 0.154 Angle : 0.663 9.497 12046 Z= 0.340 Chirality : 0.048 0.297 1302 Planarity : 0.005 0.054 1572 Dihedral : 4.839 19.850 1188 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.69 % Allowed : 23.26 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1076 helix: 1.90 (1.09), residues: 24 sheet: -0.27 (0.27), residues: 356 loop : 0.26 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 364 TYR 0.019 0.001 TYR C 59 PHE 0.010 0.001 PHE A 426 TRP 0.012 0.001 TRP B 308 HIS 0.003 0.000 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 8816) covalent geometry : angle 0.66268 / 0.34 (12038) SS BOND : bond 0.00251 / 0.13 ( 4) SS BOND : angle 0.77959 / 0.37 ( 8) hydrogen bonds : bond 0.03064 / 1.97 ( 240) hydrogen bonds : angle 6.37314 / 4.44 ( 642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2638.21 seconds wall clock time: 45 minutes 51.37 seconds (2751.37 seconds total)