Starting phenix.real_space_refine on Fri May 9 15:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzs_51733/05_2025/9gzs_51733.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzs_51733/05_2025/9gzs_51733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gzs_51733/05_2025/9gzs_51733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzs_51733/05_2025/9gzs_51733.map" model { file = "/net/cci-nas-00/data/ceres_data/9gzs_51733/05_2025/9gzs_51733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzs_51733/05_2025/9gzs_51733.cif" } resolution = 3.1 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= 0.000 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: 3 Type Number sf(0) Gaussians C 1854 2.51 5 N 534 2.21 5 O 612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3000 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 179 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 135 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Restraints were copied for chains: D, G, J, M, P, E, H, K, N, Q, F, I, L, O, R Time building chain proxies: 1.99, per 1000 atoms: 0.66 Number of scatterers: 3000 At special positions: 0 Unit cell: (95.36, 70.03, 49.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 612 8.00 N 534 7.00 C 1854 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 332.4 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 58.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 22 removed outlier: 6.233A pdb=" N PHE A 15 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N HIS D 18 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 17 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N SER D 20 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER A 19 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ASN D 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN A 21 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE D 15 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS G 18 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL D 17 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N SER G 20 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER D 19 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASN G 22 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN D 21 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE G 15 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N HIS J 18 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL G 17 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER J 20 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER G 19 " --> pdb=" O SER J 20 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASN J 22 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN G 21 " --> pdb=" O ASN J 22 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE J 15 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N HIS M 18 " --> pdb=" O PHE J 15 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL J 17 " --> pdb=" O HIS M 18 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N SER M 20 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER J 19 " --> pdb=" O SER M 20 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ASN M 22 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN J 21 " --> pdb=" O ASN M 22 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE M 15 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N HIS P 18 " --> pdb=" O PHE M 15 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL M 17 " --> pdb=" O HIS P 18 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N SER P 20 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER M 19 " --> pdb=" O SER P 20 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASN P 22 " --> pdb=" O SER M 19 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN M 21 " --> pdb=" O ASN P 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 33 removed outlier: 6.471A pdb=" N LEU D 27 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR G 30 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER D 29 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL G 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN D 31 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU J 27 " --> pdb=" O SER M 28 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR M 30 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER J 29 " --> pdb=" O THR M 30 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL M 32 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN J 31 " --> pdb=" O VAL M 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33 removed outlier: 6.538A pdb=" N LEU B 27 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N THR E 30 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER B 29 " --> pdb=" O THR E 30 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL E 32 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN B 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU E 27 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N THR H 30 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER E 29 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL H 32 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN E 31 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU H 27 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N THR K 30 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER H 29 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL K 32 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN H 31 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU K 27 " --> pdb=" O SER N 28 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N THR N 30 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER K 29 " --> pdb=" O THR N 30 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL N 32 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN K 31 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU N 27 " --> pdb=" O SER Q 28 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR Q 30 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER N 29 " --> pdb=" O THR Q 30 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL Q 32 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN N 31 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 20 removed outlier: 6.448A pdb=" N PHE C 15 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N HIS F 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL C 17 " --> pdb=" O HIS F 18 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER F 20 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER C 19 " --> pdb=" O SER F 20 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE F 15 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N HIS I 18 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL F 17 " --> pdb=" O HIS I 18 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N SER I 20 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER F 19 " --> pdb=" O SER I 20 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE I 15 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N HIS L 18 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL I 17 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N SER L 20 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER I 19 " --> pdb=" O SER L 20 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE L 15 " --> pdb=" O LEU O 16 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS O 18 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL L 17 " --> pdb=" O HIS O 18 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER O 20 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER L 19 " --> pdb=" O SER O 20 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 25 through 30 removed outlier: 6.294A pdb=" N ILE C 26 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N SER F 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER C 28 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE I 26 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER L 29 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER I 28 " --> pdb=" O SER L 29 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE O 26 " --> pdb=" O LEU R 27 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N SER R 29 " --> pdb=" O ILE O 26 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER O 28 " --> pdb=" O SER R 29 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 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: 0.66 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 486 1.29 - 1.35: 504 1.35 - 1.41: 382 1.41 - 1.48: 500 1.48 - 1.54: 1164 Bond restraints: 3036 Sorted by residual: bond pdb=" CG LEU Q 16 " pdb=" CD2 LEU Q 16 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.49e+00 bond pdb=" CG LEU K 16 " pdb=" CD2 LEU K 16 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.49e+00 bond pdb=" CG LEU E 16 " pdb=" CD2 LEU E 16 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.49e+00 bond pdb=" CG LEU H 16 " pdb=" CD2 LEU H 16 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.48e+00 bond pdb=" CG LEU N 16 " pdb=" CD2 LEU N 16 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.34e+00 ... (remaining 3031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 3653 1.20 - 2.41: 360 2.41 - 3.61: 82 3.61 - 4.81: 13 4.81 - 6.02: 8 Bond angle restraints: 4116 Sorted by residual: angle pdb=" N VAL J 17 " pdb=" CA VAL J 17 " pdb=" C VAL J 17 " ideal model delta sigma weight residual 108.12 111.56 -3.44 1.44e+00 4.82e-01 5.69e+00 angle pdb=" N VAL D 17 " pdb=" CA VAL D 17 " pdb=" C VAL D 17 " ideal model delta sigma weight residual 108.12 111.53 -3.41 1.44e+00 4.82e-01 5.60e+00 angle pdb=" N GLY M 24 " pdb=" CA GLY M 24 " pdb=" C GLY M 24 " ideal model delta sigma weight residual 111.04 115.22 -4.18 1.77e+00 3.19e-01 5.57e+00 angle pdb=" N VAL P 17 " pdb=" CA VAL P 17 " pdb=" C VAL P 17 " ideal model delta sigma weight residual 108.12 111.52 -3.40 1.44e+00 4.82e-01 5.57e+00 angle pdb=" N GLY J 24 " pdb=" CA GLY J 24 " pdb=" C GLY J 24 " ideal model delta sigma weight residual 111.04 115.21 -4.17 1.77e+00 3.19e-01 5.55e+00 ... (remaining 4111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.60: 1305 6.60 - 13.19: 177 13.19 - 19.79: 108 19.79 - 26.38: 60 26.38 - 32.98: 42 Dihedral angle restraints: 1692 sinusoidal: 552 harmonic: 1140 Sorted by residual: dihedral pdb=" CA LEU F 16 " pdb=" CB LEU F 16 " pdb=" CG LEU F 16 " pdb=" CD1 LEU F 16 " ideal model delta sinusoidal sigma weight residual 180.00 147.02 32.98 3 1.50e+01 4.44e-03 5.48e+00 dihedral pdb=" CA LEU I 16 " pdb=" CB LEU I 16 " pdb=" CG LEU I 16 " pdb=" CD1 LEU I 16 " ideal model delta sinusoidal sigma weight residual 180.00 147.04 32.96 3 1.50e+01 4.44e-03 5.47e+00 dihedral pdb=" CA LEU C 16 " pdb=" CB LEU C 16 " pdb=" CG LEU C 16 " pdb=" CD1 LEU C 16 " ideal model delta sinusoidal sigma weight residual 180.00 147.04 32.96 3 1.50e+01 4.44e-03 5.47e+00 ... (remaining 1689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 398 0.083 - 0.167: 82 0.167 - 0.250: 0 0.250 - 0.333: 0 0.333 - 0.417: 6 Chirality restraints: 486 Sorted by residual: chirality pdb=" CG LEU K 16 " pdb=" CB LEU K 16 " pdb=" CD1 LEU K 16 " pdb=" CD2 LEU K 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CG LEU N 16 " pdb=" CB LEU N 16 " pdb=" CD1 LEU N 16 " pdb=" CD2 LEU N 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CG LEU H 16 " pdb=" CB LEU H 16 " pdb=" CD1 LEU H 16 " pdb=" CD2 LEU H 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 483 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 15 " -0.011 2.00e-02 2.50e+03 1.03e-02 1.86e+00 pdb=" CG PHE E 15 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE E 15 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 15 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 15 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 15 " -0.011 2.00e-02 2.50e+03 1.03e-02 1.84e+00 pdb=" CG PHE H 15 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE H 15 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE H 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE H 15 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 15 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 15 " -0.011 2.00e-02 2.50e+03 1.01e-02 1.80e+00 pdb=" CG PHE K 15 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE K 15 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE K 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE K 15 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE K 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 15 " -0.003 2.00e-02 2.50e+03 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.66 - 3.11: 2228 3.11 - 3.56: 2950 3.56 - 4.00: 4442 4.00 - 4.45: 5412 4.45 - 4.90: 9930 Nonbonded interactions: 24962 Sorted by model distance: nonbonded pdb=" N NH2 D 38 " pdb=" O TYR G 37 " model vdw 2.658 3.120 nonbonded pdb=" C SER M 19 " pdb=" OG SER M 19 " model vdw 2.676 2.616 nonbonded pdb=" C SER D 19 " pdb=" OG SER D 19 " model vdw 2.677 2.616 nonbonded pdb=" C SER A 19 " pdb=" OG SER A 19 " model vdw 2.677 2.616 nonbonded pdb=" C SER G 19 " pdb=" OG SER G 19 " model vdw 2.677 2.616 ... (remaining 24957 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' } 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: 1.450 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.860 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.009 0.105 3048 Z= 0.686 Angle : 0.831 6.017 4116 Z= 0.490 Chirality : 0.072 0.417 486 Planarity : 0.003 0.010 534 Dihedral : 11.045 32.980 948 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.45 % Allowed : 12.07 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.04 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 18 PHE 0.024 0.004 PHE E 15 TYR 0.013 0.003 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.12035 ( 71) hydrogen bonds : angle 6.06057 ( 213) covalent geometry : bond 0.00605 ( 3036) covalent geometry : angle 0.83060 ( 4116) Misc. bond : bond 0.10330 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 9 time to evaluate : 0.334 Fit side-chains REVERT: G 31 ASN cc_start: 0.7657 (m-40) cc_final: 0.7101 (t0) outliers start: 12 outliers final: 3 residues processed: 21 average time/residue: 0.0705 time to fit residues: 2.5070 Evaluate side-chains 8 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 5 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain N residue 28 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN B 21 ASN C 31 ASN D 21 ASN E 21 ASN F 31 ASN G 21 ASN H 21 ASN I 31 ASN J 21 ASN K 21 ASN L 31 ASN M 21 ASN N 21 ASN O 31 ASN P 21 ASN Q 21 ASN R 31 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.095759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076401 restraints weight = 4556.237| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.38 r_work: 0.3320 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3048 Z= 0.209 Angle : 0.600 6.998 4116 Z= 0.318 Chirality : 0.048 0.125 486 Planarity : 0.002 0.007 534 Dihedral : 4.806 14.361 399 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.63 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 18 PHE 0.016 0.002 PHE N 15 TYR 0.003 0.001 TYR H 37 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 71) hydrogen bonds : angle 4.55403 ( 213) covalent geometry : bond 0.00468 ( 3036) covalent geometry : angle 0.60031 ( 4116) Misc. bond : bond 0.00133 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0739 time to fit residues: 1.4288 Evaluate side-chains 2 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.094885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075560 restraints weight = 4553.230| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.34 r_work: 0.3303 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3048 Z= 0.230 Angle : 0.581 6.109 4116 Z= 0.315 Chirality : 0.047 0.125 486 Planarity : 0.002 0.006 534 Dihedral : 4.995 14.140 396 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % 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: -2.95 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 18 PHE 0.015 0.003 PHE K 15 TYR 0.005 0.001 TYR M 37 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 71) hydrogen bonds : angle 4.33398 ( 213) covalent geometry : bond 0.00511 ( 3036) covalent geometry : angle 0.58099 ( 4116) Misc. bond : bond 0.00125 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.334 Fit side-chains REVERT: L 19 SER cc_start: 0.9059 (m) cc_final: 0.8824 (t) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0684 time to fit residues: 1.3698 Evaluate side-chains 5 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.093988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073719 restraints weight = 4778.534| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.39 r_work: 0.3254 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 3048 Z= 0.419 Angle : 0.666 5.534 4116 Z= 0.383 Chirality : 0.051 0.132 486 Planarity : 0.004 0.010 534 Dihedral : 5.518 15.148 396 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.01 % Allowed : 13.51 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.77 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.20), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS R 18 PHE 0.020 0.004 PHE K 15 TYR 0.011 0.002 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 71) hydrogen bonds : angle 4.44041 ( 213) covalent geometry : bond 0.00912 ( 3036) covalent geometry : angle 0.66563 ( 4116) Misc. bond : bond 0.00274 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 5 time to evaluate : 0.338 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 12 average time/residue: 0.0611 time to fit residues: 1.5724 Evaluate side-chains 12 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 5 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain Q residue 34 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.096351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.075500 restraints weight = 4820.978| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.47 r_work: 0.3283 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3048 Z= 0.197 Angle : 0.529 4.991 4116 Z= 0.292 Chirality : 0.045 0.119 486 Planarity : 0.002 0.006 534 Dihedral : 4.639 12.985 396 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.72 % Allowed : 15.23 % Favored : 83.05 % 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: -3.71 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS O 18 PHE 0.014 0.002 PHE K 15 TYR 0.006 0.001 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 71) hydrogen bonds : angle 4.01005 ( 213) covalent geometry : bond 0.00432 ( 3036) covalent geometry : angle 0.52869 ( 4116) Misc. bond : bond 0.00129 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 5 time to evaluate : 0.342 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 11 average time/residue: 0.0575 time to fit residues: 1.3854 Evaluate side-chains 8 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 3 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain P residue 34 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.095009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.074404 restraints weight = 5089.598| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.43 r_work: 0.3253 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3048 Z= 0.319 Angle : 0.590 4.764 4116 Z= 0.336 Chirality : 0.048 0.130 486 Planarity : 0.003 0.007 534 Dihedral : 5.006 14.053 396 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.87 % Allowed : 14.08 % Favored : 83.05 % 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: -3.95 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS R 18 PHE 0.016 0.003 PHE Q 15 TYR 0.011 0.002 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 71) hydrogen bonds : angle 4.01149 ( 213) covalent geometry : bond 0.00693 ( 3036) covalent geometry : angle 0.59003 ( 4116) Misc. bond : bond 0.00207 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1 time to evaluate : 0.331 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 11 average time/residue: 0.0544 time to fit residues: 1.3969 Evaluate side-chains 11 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain Q residue 34 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.095830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.074925 restraints weight = 4608.951| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.42 r_work: 0.3267 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3048 Z= 0.246 Angle : 0.548 4.524 4116 Z= 0.308 Chirality : 0.046 0.124 486 Planarity : 0.002 0.006 534 Dihedral : 4.781 12.726 396 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.16 % Allowed : 13.22 % Favored : 83.62 % 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: -3.92 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS O 18 PHE 0.014 0.002 PHE K 15 TYR 0.009 0.002 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 71) hydrogen bonds : angle 3.83902 ( 213) covalent geometry : bond 0.00538 ( 3036) covalent geometry : angle 0.54770 ( 4116) Misc. bond : bond 0.00163 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 3 time to evaluate : 0.322 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 14 average time/residue: 0.0584 time to fit residues: 1.6461 Evaluate side-chains 12 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 2 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain Q residue 34 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 0.0970 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.096806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.076096 restraints weight = 4320.389| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.34 r_work: 0.3290 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3048 Z= 0.184 Angle : 0.526 7.965 4116 Z= 0.286 Chirality : 0.045 0.119 486 Planarity : 0.002 0.006 534 Dihedral : 4.470 12.989 396 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.30 % Allowed : 14.37 % Favored : 83.33 % 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 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS O 18 PHE 0.013 0.002 PHE K 15 TYR 0.007 0.001 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 71) hydrogen bonds : angle 3.74712 ( 213) covalent geometry : bond 0.00405 ( 3036) covalent geometry : angle 0.52562 ( 4116) Misc. bond : bond 0.00123 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 4 time to evaluate : 0.331 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 12 average time/residue: 0.0608 time to fit residues: 1.5366 Evaluate side-chains 12 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 4 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.095721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.074184 restraints weight = 4832.253| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.50 r_work: 0.3250 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3048 Z= 0.286 Angle : 0.569 7.103 4116 Z= 0.321 Chirality : 0.047 0.127 486 Planarity : 0.003 0.007 534 Dihedral : 4.799 13.402 396 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.45 % Allowed : 13.51 % Favored : 83.05 % 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: -4.00 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS R 18 PHE 0.015 0.003 PHE Q 15 TYR 0.011 0.002 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 71) hydrogen bonds : angle 3.84162 ( 213) covalent geometry : bond 0.00623 ( 3036) covalent geometry : angle 0.56865 ( 4116) Misc. bond : bond 0.00189 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 4 time to evaluate : 0.318 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 16 average time/residue: 0.0579 time to fit residues: 1.8246 Evaluate side-chains 15 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 3 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain Q residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.098198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.077109 restraints weight = 4261.613| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.36 r_work: 0.3293 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3048 Z= 0.141 Angle : 0.506 7.252 4116 Z= 0.273 Chirality : 0.045 0.118 486 Planarity : 0.002 0.006 534 Dihedral : 4.317 12.546 396 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.01 % Allowed : 15.23 % Favored : 82.76 % 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: -3.72 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 18 PHE 0.013 0.002 PHE K 15 TYR 0.005 0.001 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 71) hydrogen bonds : angle 3.57570 ( 213) covalent geometry : bond 0.00313 ( 3036) covalent geometry : angle 0.50551 ( 4116) Misc. bond : bond 0.00093 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 6 time to evaluate : 0.355 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 13 average time/residue: 0.0622 time to fit residues: 1.6410 Evaluate side-chains 12 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 5 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain Q residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.095645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074619 restraints weight = 4321.040| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.34 r_work: 0.3248 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3048 Z= 0.337 Angle : 0.610 7.053 4116 Z= 0.344 Chirality : 0.048 0.140 486 Planarity : 0.003 0.007 534 Dihedral : 4.812 14.104 396 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.87 % Allowed : 14.66 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS R 18 PHE 0.016 0.003 PHE Q 15 TYR 0.013 0.002 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 71) hydrogen bonds : angle 3.72387 ( 213) covalent geometry : bond 0.00733 ( 3036) covalent geometry : angle 0.61000 ( 4116) Misc. bond : bond 0.00224 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.20 seconds wall clock time: 30 minutes 33.24 seconds (1833.24 seconds total)