Starting phenix.real_space_refine on Wed Sep 17 04:12:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzt_51734/09_2025/9gzt_51734.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzt_51734/09_2025/9gzt_51734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gzt_51734/09_2025/9gzt_51734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzt_51734/09_2025/9gzt_51734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gzt_51734/09_2025/9gzt_51734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzt_51734/09_2025/9gzt_51734.map" } resolution = 2.9 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: 3 Type Number sf(0) Gaussians C 2436 2.51 5 N 696 2.21 5 O 792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3924 Number of models: 1 Model: "" Number of chains: 3 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: "C" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 142 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Restraints were copied for chains: B, E, F, I, J, M, N, Q, R, U, V, D, G, H, K, L, O, P, S, T, W, X Time building chain proxies: 0.62, per 1000 atoms: 0.16 Number of scatterers: 3924 At special positions: 0 Unit cell: (122.925, 74.5, 47.68, 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 792 8.00 N 696 7.00 C 2436 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: 0.35 Conformation dependent library (CDL) restraints added in 150.3 milliseconds Enol-peptide restraints added in 1.4 microseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 59.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 33 removed outlier: 6.520A pdb=" N LEU A 27 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR E 30 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER A 29 " --> pdb=" O THR E 30 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL E 32 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN A 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU E 27 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR I 30 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER E 29 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL I 32 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN E 31 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU I 27 " --> pdb=" O SER M 28 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N THR M 30 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER I 29 " --> pdb=" O THR M 30 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL M 32 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN I 31 " --> pdb=" O VAL M 32 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU M 27 " --> pdb=" O SER Q 28 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N THR Q 30 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER M 29 " --> pdb=" O THR Q 30 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL Q 32 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN M 31 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU Q 27 " --> pdb=" O SER U 28 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR U 30 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER Q 29 " --> pdb=" O THR U 30 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL U 32 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN Q 31 " --> pdb=" O VAL U 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 14 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33 removed outlier: 6.516A pdb=" N LEU B 27 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR F 30 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER B 29 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL F 32 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN B 31 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU F 27 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR J 30 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER F 29 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL J 32 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN F 31 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU J 27 " --> pdb=" O SER N 28 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR N 30 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER J 29 " --> pdb=" O THR N 30 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL N 32 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN J 31 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU N 27 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR R 30 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER N 29 " --> pdb=" O THR R 30 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL R 32 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN N 31 " --> pdb=" O VAL R 32 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU R 27 " --> pdb=" O SER V 28 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR V 30 " --> pdb=" O LEU R 27 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER R 29 " --> pdb=" O THR V 30 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL V 32 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN R 31 " --> pdb=" O VAL V 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: 6.439A pdb=" N PHE C 15 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS G 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL C 17 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N SER G 20 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER C 19 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE G 15 " --> pdb=" O LEU K 16 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS K 18 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL G 17 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER K 20 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER G 19 " --> pdb=" O SER K 20 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE K 15 " --> pdb=" O LEU O 16 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N HIS O 18 " --> pdb=" O PHE K 15 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL K 17 " --> pdb=" O HIS O 18 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER O 20 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER K 19 " --> pdb=" O SER O 20 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE S 15 " --> pdb=" O LEU W 16 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N HIS W 18 " --> pdb=" O PHE S 15 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL S 17 " --> pdb=" O HIS W 18 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER W 20 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER S 19 " --> pdb=" O SER W 20 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 25 through 31 removed outlier: 6.296A pdb=" N ILE K 26 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N SER O 29 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER K 28 " --> pdb=" O SER O 29 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASN O 31 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR K 30 " --> pdb=" O ASN O 31 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE O 26 " --> pdb=" O LEU S 27 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N SER S 29 " --> pdb=" O ILE O 26 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER O 28 " --> pdb=" O SER S 29 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN S 31 " --> pdb=" O SER O 28 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR O 30 " --> pdb=" O ASN S 31 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 15 through 20 removed outlier: 6.663A pdb=" N PHE D 15 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N HIS H 18 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL D 17 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER H 20 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER D 19 " --> pdb=" O SER H 20 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE H 15 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS L 18 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL H 17 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER L 20 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER H 19 " --> pdb=" O SER L 20 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE L 15 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N HIS P 18 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL L 17 " --> pdb=" O HIS P 18 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N SER P 20 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER L 19 " --> pdb=" O SER P 20 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE P 15 " --> pdb=" O LEU T 16 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS T 18 " --> pdb=" O PHE P 15 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL P 17 " --> pdb=" O HIS T 18 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N SER T 20 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER P 19 " --> pdb=" O SER T 20 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE T 15 " --> pdb=" O LEU X 16 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N HIS X 18 " --> pdb=" O PHE T 15 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL T 17 " --> pdb=" O HIS X 18 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N SER X 20 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER T 19 " --> pdb=" O SER X 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 25 through 31 removed outlier: 6.408A pdb=" N ILE P 26 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N SER T 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER P 28 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASN T 31 " --> pdb=" O SER P 28 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR P 30 " --> pdb=" O ASN T 31 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 381 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: 0.73 Time building geometry restraints manager: 0.46 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: 636 1.29 - 1.35: 660 1.35 - 1.41: 501 1.41 - 1.48: 627 1.48 - 1.54: 1548 Bond restraints: 3972 Sorted by residual: bond pdb=" CG1 ILE Q 26 " pdb=" CD1 ILE Q 26 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.02e+00 bond pdb=" CG1 ILE R 26 " pdb=" CD1 ILE R 26 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.01e+00 bond pdb=" CG1 ILE E 26 " pdb=" CD1 ILE E 26 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.00e+00 bond pdb=" CG1 ILE A 26 " pdb=" CD1 ILE A 26 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.00e+00 bond pdb=" CG1 ILE M 26 " pdb=" CD1 ILE M 26 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.94e-01 ... (remaining 3967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 4421 0.86 - 1.71: 618 1.71 - 2.57: 217 2.57 - 3.42: 84 3.42 - 4.28: 48 Bond angle restraints: 5388 Sorted by residual: angle pdb=" N VAL Q 17 " pdb=" CA VAL Q 17 " pdb=" C VAL Q 17 " ideal model delta sigma weight residual 108.17 112.05 -3.88 1.46e+00 4.69e-01 7.05e+00 angle pdb=" N VAL B 17 " pdb=" CA VAL B 17 " pdb=" C VAL B 17 " ideal model delta sigma weight residual 108.17 112.02 -3.85 1.46e+00 4.69e-01 6.97e+00 angle pdb=" N VAL E 17 " pdb=" CA VAL E 17 " pdb=" C VAL E 17 " ideal model delta sigma weight residual 108.17 112.02 -3.85 1.46e+00 4.69e-01 6.95e+00 angle pdb=" N VAL F 17 " pdb=" CA VAL F 17 " pdb=" C VAL F 17 " ideal model delta sigma weight residual 108.17 112.01 -3.84 1.46e+00 4.69e-01 6.92e+00 angle pdb=" N VAL M 17 " pdb=" CA VAL M 17 " pdb=" C VAL M 17 " ideal model delta sigma weight residual 108.17 112.00 -3.83 1.46e+00 4.69e-01 6.89e+00 ... (remaining 5383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.61: 1716 6.61 - 13.22: 276 13.22 - 19.82: 108 19.82 - 26.43: 36 26.43 - 33.04: 84 Dihedral angle restraints: 2220 sinusoidal: 720 harmonic: 1500 Sorted by residual: dihedral pdb=" CA LEU W 16 " pdb=" CB LEU W 16 " pdb=" CG LEU W 16 " pdb=" CD1 LEU W 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 180.00 147.05 32.95 3 1.50e+01 4.44e-03 5.47e+00 dihedral pdb=" CA LEU K 16 " pdb=" CB LEU K 16 " pdb=" CG LEU K 16 " pdb=" CD1 LEU K 16 " ideal model delta sinusoidal sigma weight residual 180.00 147.06 32.94 3 1.50e+01 4.44e-03 5.47e+00 ... (remaining 2217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 400 0.033 - 0.066: 115 0.066 - 0.100: 76 0.100 - 0.133: 41 0.133 - 0.166: 16 Chirality restraints: 648 Sorted by residual: chirality pdb=" CB VAL P 32 " pdb=" CA VAL P 32 " pdb=" CG1 VAL P 32 " pdb=" CG2 VAL P 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CB VAL D 32 " pdb=" CA VAL D 32 " pdb=" CG1 VAL D 32 " pdb=" CG2 VAL D 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CB VAL H 32 " pdb=" CA VAL H 32 " pdb=" CG1 VAL H 32 " pdb=" CG2 VAL H 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 645 not shown) Planarity restraints: 696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 23 " 0.008 2.00e-02 2.50e+03 6.58e-03 7.57e-01 pdb=" CG PHE H 23 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE H 23 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE H 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 23 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 15 " -0.009 2.00e-02 2.50e+03 6.58e-03 7.57e-01 pdb=" CG PHE N 15 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE N 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE N 15 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE N 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE N 15 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE N 15 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 15 " -0.009 2.00e-02 2.50e+03 6.55e-03 7.51e-01 pdb=" CG PHE A 15 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE A 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 15 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 15 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 15 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 15 " -0.002 2.00e-02 2.50e+03 ... (remaining 693 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 2559 3.06 - 3.52: 3563 3.52 - 3.98: 5880 3.98 - 4.44: 6857 4.44 - 4.90: 12809 Nonbonded interactions: 31668 Sorted by model distance: nonbonded pdb=" O ASN T 22 " pdb=" N PHE X 23 " model vdw 2.597 3.120 nonbonded pdb=" N NH2 Q 38 " pdb=" O TYR U 37 " model vdw 2.661 3.120 nonbonded pdb=" N VAL D 32 " pdb=" O VAL D 32 " model vdw 2.665 2.496 nonbonded pdb=" N VAL L 32 " pdb=" O VAL L 32 " model vdw 2.666 2.496 nonbonded pdb=" N VAL H 32 " pdb=" O VAL H 32 " model vdw 2.666 2.496 ... (remaining 31663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' } 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: 2.530 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.560 Find NCS groups from input model: 0.040 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.007 0.104 3984 Z= 0.604 Angle : 0.841 4.281 5388 Z= 0.507 Chirality : 0.054 0.166 648 Planarity : 0.002 0.007 696 Dihedral : 10.897 33.041 1236 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.24), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.18), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR U 37 PHE 0.015 0.003 PHE H 23 HIS 0.003 0.001 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 3972) covalent geometry : angle 0.84091 ( 5388) hydrogen bonds : bond 0.16256 ( 127) hydrogen bonds : angle 7.63613 ( 381) Misc. bond : bond 0.10345 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.148 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0644 time to fit residues: 4.2870 Evaluate side-chains 26 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN D 21 ASN E 18 HIS F 18 HIS G 21 ASN H 21 ASN I 18 HIS I 35 ASN J 18 HIS K 21 ASN L 21 ASN M 18 HIS N 18 HIS O 21 ASN P 21 ASN Q 18 HIS R 18 HIS R 31 ASN S 21 ASN T 21 ASN W 21 ASN X 21 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.111898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085714 restraints weight = 5762.028| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.47 r_work: 0.3340 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3984 Z= 0.157 Angle : 0.549 6.237 5388 Z= 0.294 Chirality : 0.044 0.123 648 Planarity : 0.002 0.006 696 Dihedral : 5.374 19.044 516 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.95 % Allowed : 8.99 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.24), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.18), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 37 PHE 0.009 0.002 PHE B 23 HIS 0.002 0.001 HIS R 18 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3972) covalent geometry : angle 0.54927 ( 5388) hydrogen bonds : bond 0.03029 ( 127) hydrogen bonds : angle 4.81386 ( 381) Misc. bond : bond 0.00122 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 15 time to evaluate : 0.161 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 28 average time/residue: 0.0315 time to fit residues: 1.5507 Evaluate side-chains 21 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain P residue 30 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.0170 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 0.0030 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 overall best weight: 3.6034 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.111464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.084881 restraints weight = 5661.772| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.46 r_work: 0.3323 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3984 Z= 0.176 Angle : 0.512 4.751 5388 Z= 0.285 Chirality : 0.043 0.125 648 Planarity : 0.002 0.005 696 Dihedral : 5.490 19.569 516 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.39 % Allowed : 8.77 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.24), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.18), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR M 37 PHE 0.009 0.002 PHE R 15 HIS 0.004 0.001 HIS R 18 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 3972) covalent geometry : angle 0.51209 ( 5388) hydrogen bonds : bond 0.03321 ( 127) hydrogen bonds : angle 4.47427 ( 381) Misc. bond : bond 0.00128 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 12 time to evaluate : 0.153 Fit side-chains REVERT: P 30 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.7756 (p) outliers start: 20 outliers final: 18 residues processed: 25 average time/residue: 0.0277 time to fit residues: 1.3189 Evaluate side-chains 31 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 12 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.103471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078258 restraints weight = 5944.308| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.46 r_work: 0.3291 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 3984 Z= 0.366 Angle : 0.613 4.000 5388 Z= 0.351 Chirality : 0.046 0.125 648 Planarity : 0.002 0.006 696 Dihedral : 6.056 20.777 516 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.36 % Allowed : 12.28 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.70 (0.24), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.18), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR M 37 PHE 0.014 0.003 PHE S 23 HIS 0.006 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00803 ( 3972) covalent geometry : angle 0.61315 ( 5388) hydrogen bonds : bond 0.04544 ( 127) hydrogen bonds : angle 4.57085 ( 381) Misc. bond : bond 0.00235 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 25 time to evaluate : 0.190 Fit side-chains REVERT: P 30 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.7892 (p) outliers start: 29 outliers final: 25 residues processed: 46 average time/residue: 0.0255 time to fit residues: 2.1112 Evaluate side-chains 51 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 25 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.105714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079429 restraints weight = 5765.962| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.59 r_work: 0.3323 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3984 Z= 0.191 Angle : 0.485 3.066 5388 Z= 0.280 Chirality : 0.043 0.126 648 Planarity : 0.002 0.005 696 Dihedral : 5.523 19.738 516 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.29 % Allowed : 19.30 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.59 (0.25), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR N 37 PHE 0.008 0.002 PHE M 15 HIS 0.003 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 3972) covalent geometry : angle 0.48532 ( 5388) hydrogen bonds : bond 0.03394 ( 127) hydrogen bonds : angle 4.30460 ( 381) Misc. bond : bond 0.00123 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 13 time to evaluate : 0.162 Fit side-chains REVERT: K 30 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7603 (p) REVERT: P 30 THR cc_start: 0.8392 (t) cc_final: 0.7876 (p) outliers start: 15 outliers final: 13 residues processed: 23 average time/residue: 0.0267 time to fit residues: 1.2233 Evaluate side-chains 27 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 13 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.104854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078609 restraints weight = 5997.433| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.61 r_work: 0.3307 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3984 Z= 0.260 Angle : 0.518 3.149 5388 Z= 0.301 Chirality : 0.044 0.127 648 Planarity : 0.002 0.006 696 Dihedral : 5.757 20.452 516 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.70 % Allowed : 17.98 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.62 (0.25), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.19), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR M 37 PHE 0.010 0.002 PHE M 15 HIS 0.004 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 3972) covalent geometry : angle 0.51830 ( 5388) hydrogen bonds : bond 0.03891 ( 127) hydrogen bonds : angle 4.41664 ( 381) Misc. bond : bond 0.00161 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 18 time to evaluate : 0.098 Fit side-chains REVERT: K 30 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7601 (p) REVERT: P 30 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.7884 (p) REVERT: U 34 SER cc_start: 0.9098 (OUTLIER) cc_final: 0.8612 (t) outliers start: 26 outliers final: 23 residues processed: 38 average time/residue: 0.0265 time to fit residues: 1.8395 Evaluate side-chains 44 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 18 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.107529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.081023 restraints weight = 6469.440| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.58 r_work: 0.3277 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 3984 Z= 0.372 Angle : 0.585 3.666 5388 Z= 0.340 Chirality : 0.044 0.129 648 Planarity : 0.002 0.006 696 Dihedral : 6.021 20.563 516 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 5.92 % Allowed : 18.86 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.72 (0.25), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.19), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR N 37 PHE 0.014 0.003 PHE P 23 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00801 ( 3972) covalent geometry : angle 0.58451 ( 5388) hydrogen bonds : bond 0.04583 ( 127) hydrogen bonds : angle 4.60097 ( 381) Misc. bond : bond 0.00225 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 20 time to evaluate : 0.184 Fit side-chains REVERT: J 29 SER cc_start: 0.9279 (OUTLIER) cc_final: 0.9026 (m) REVERT: K 30 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7647 (p) REVERT: M 34 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8560 (t) REVERT: P 30 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.7913 (p) REVERT: U 34 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8664 (t) outliers start: 27 outliers final: 22 residues processed: 41 average time/residue: 0.0216 time to fit residues: 1.6449 Evaluate side-chains 45 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 18 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.109094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.082315 restraints weight = 6578.305| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.65 r_work: 0.3297 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3984 Z= 0.213 Angle : 0.488 3.024 5388 Z= 0.284 Chirality : 0.043 0.129 648 Planarity : 0.002 0.005 696 Dihedral : 5.659 19.910 516 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.48 % Allowed : 19.52 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.68 (0.26), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.20), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR N 37 PHE 0.009 0.002 PHE M 15 HIS 0.003 0.001 HIS R 18 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 3972) covalent geometry : angle 0.48755 ( 5388) hydrogen bonds : bond 0.03594 ( 127) hydrogen bonds : angle 4.39669 ( 381) Misc. bond : bond 0.00135 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 16 time to evaluate : 0.135 Fit side-chains REVERT: E 34 SER cc_start: 0.9135 (OUTLIER) cc_final: 0.8628 (t) REVERT: K 30 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7618 (p) REVERT: M 34 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8524 (t) REVERT: P 30 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.7893 (p) REVERT: U 34 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8637 (t) outliers start: 25 outliers final: 19 residues processed: 37 average time/residue: 0.0251 time to fit residues: 1.7201 Evaluate side-chains 40 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 16 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 overall best weight: 4.8986 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.104366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078394 restraints weight = 6116.815| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.58 r_work: 0.3291 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3984 Z= 0.249 Angle : 0.505 3.182 5388 Z= 0.294 Chirality : 0.043 0.129 648 Planarity : 0.002 0.006 696 Dihedral : 5.744 20.101 516 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 5.48 % Allowed : 19.30 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.71 (0.26), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.20), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR N 37 PHE 0.010 0.002 PHE M 15 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 3972) covalent geometry : angle 0.50531 ( 5388) hydrogen bonds : bond 0.03799 ( 127) hydrogen bonds : angle 4.43487 ( 381) Misc. bond : bond 0.00151 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 16 time to evaluate : 0.096 Fit side-chains REVERT: E 34 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8656 (t) REVERT: I 29 SER cc_start: 0.9221 (OUTLIER) cc_final: 0.8877 (m) REVERT: J 29 SER cc_start: 0.9253 (OUTLIER) cc_final: 0.8990 (m) REVERT: K 30 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7609 (p) REVERT: M 34 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8537 (t) REVERT: P 30 THR cc_start: 0.8403 (t) cc_final: 0.7872 (p) REVERT: U 34 SER cc_start: 0.9133 (OUTLIER) cc_final: 0.8651 (t) REVERT: V 34 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8683 (t) outliers start: 25 outliers final: 17 residues processed: 38 average time/residue: 0.0249 time to fit residues: 1.7136 Evaluate side-chains 40 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 16 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.104691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077898 restraints weight = 6205.618| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.68 r_work: 0.3275 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 3984 Z= 0.365 Angle : 0.574 3.629 5388 Z= 0.334 Chirality : 0.044 0.131 648 Planarity : 0.002 0.006 696 Dihedral : 6.035 20.474 516 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 5.48 % Allowed : 19.52 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (0.26), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.19), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR N 37 PHE 0.013 0.003 PHE L 23 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00782 ( 3972) covalent geometry : angle 0.57420 ( 5388) hydrogen bonds : bond 0.04497 ( 127) hydrogen bonds : angle 4.55116 ( 381) Misc. bond : bond 0.00224 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 17 time to evaluate : 0.143 Fit side-chains REVERT: A 29 SER cc_start: 0.9299 (t) cc_final: 0.9049 (m) REVERT: I 29 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.8938 (m) REVERT: J 29 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.9045 (m) REVERT: K 30 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7631 (p) REVERT: M 34 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8592 (t) REVERT: P 30 THR cc_start: 0.8422 (t) cc_final: 0.7880 (p) REVERT: U 34 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8688 (t) REVERT: V 34 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8699 (t) outliers start: 25 outliers final: 19 residues processed: 37 average time/residue: 0.0248 time to fit residues: 1.6652 Evaluate side-chains 42 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 17 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.106809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.080104 restraints weight = 6076.204| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.69 r_work: 0.3335 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3984 Z= 0.144 Angle : 0.446 2.664 5388 Z= 0.261 Chirality : 0.043 0.128 648 Planarity : 0.001 0.004 696 Dihedral : 5.451 19.364 516 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 4.39 % Allowed : 20.83 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.66 (0.27), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.20), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR N 37 PHE 0.007 0.001 PHE M 15 HIS 0.002 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3972) covalent geometry : angle 0.44616 ( 5388) hydrogen bonds : bond 0.02974 ( 127) hydrogen bonds : angle 4.20923 ( 381) Misc. bond : bond 0.00089 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.78 seconds wall clock time: 21 minutes 59.67 seconds (1319.67 seconds total)