Starting phenix.real_space_refine on Thu Jun 4 08:22:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c53_7342/06_2026/6c53_7342.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c53_7342/06_2026/6c53_7342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6c53_7342/06_2026/6c53_7342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c53_7342/06_2026/6c53_7342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c53_7342/06_2026/6c53_7342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c53_7342/06_2026/6c53_7342.map" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= -0.010 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 7359 2.51 5 N 2112 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12023 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K Time building chain proxies: 1.54, per 1000 atoms: 0.13 Number of scatterers: 12023 At special positions: 0 Unit cell: (82.95, 82.95, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 2530 8.00 N 2112 7.00 C 7359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 61 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 61 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 61 " distance=2.03 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 61 " distance=2.03 Simple disulfide: pdb=" SG CYS K 21 " - pdb=" SG CYS K 61 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 731.7 milliseconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 43 sheets defined 3.8% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.627A pdb=" N VAL F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 29 removed outlier: 3.627A pdb=" N VAL G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL H 28 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL I 28 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL J 28 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 removed outlier: 3.627A pdb=" N VAL K 28 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN A 6 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL B 156 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 74 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 37 removed outlier: 8.331A pdb=" N VAL B 37 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU A 15 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 23 removed outlier: 3.603A pdb=" N ALA A 22 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN A 59 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN A 129 " --> pdb=" O ASN A 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.577A pdb=" N LEU A 74 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL A 156 " --> pdb=" O ASN C 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN C 6 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN B 6 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL D 156 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 74 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 36 through 37 removed outlier: 8.330A pdb=" N VAL D 37 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B 15 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA B 22 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN B 59 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B 129 " --> pdb=" O ASN B 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA C 22 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN C 59 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN C 129 " --> pdb=" O ASN C 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB4, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AB5, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU C 74 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL C 156 " --> pdb=" O ASN E 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN E 6 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN D 6 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL F 156 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 74 " --> pdb=" O THR F 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 36 through 37 removed outlier: 8.332A pdb=" N VAL F 37 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 15 " --> pdb=" O VAL F 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA D 22 " --> pdb=" O ASN D 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN D 59 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN D 129 " --> pdb=" O ASN D 59 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA E 22 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASN E 59 " --> pdb=" O ASN E 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN E 129 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 36 through 37 Processing sheet with id=AC3, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.575A pdb=" N LEU E 74 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL E 156 " --> pdb=" O ASN G 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN G 6 " --> pdb=" O VAL E 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN F 6 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL H 156 " --> pdb=" O ASN F 6 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU H 74 " --> pdb=" O THR H 153 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 36 through 37 removed outlier: 8.331A pdb=" N VAL H 37 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU F 15 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA F 22 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN F 59 " --> pdb=" O ASN F 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN F 129 " --> pdb=" O ASN F 59 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 52 through 54 Processing sheet with id=AC9, first strand: chain 'G' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA G 22 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN G 59 " --> pdb=" O ASN G 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN G 129 " --> pdb=" O ASN G 59 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 36 through 37 Processing sheet with id=AD2, first strand: chain 'G' and resid 52 through 54 Processing sheet with id=AD3, first strand: chain 'G' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU G 74 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL G 156 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN I 6 " --> pdb=" O VAL G 156 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN H 6 " --> pdb=" O VAL J 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL J 156 " --> pdb=" O ASN H 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 74 " --> pdb=" O THR J 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 36 through 37 removed outlier: 8.331A pdb=" N VAL J 37 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU H 15 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA H 22 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN H 59 " --> pdb=" O ASN H 129 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN H 129 " --> pdb=" O ASN H 59 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 52 through 54 Processing sheet with id=AD8, first strand: chain 'I' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA I 22 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN I 59 " --> pdb=" O ASN I 129 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASN I 129 " --> pdb=" O ASN I 59 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 36 through 37 Processing sheet with id=AE1, first strand: chain 'I' and resid 52 through 54 Processing sheet with id=AE2, first strand: chain 'I' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU I 74 " --> pdb=" O THR I 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL I 156 " --> pdb=" O ASN K 6 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN K 6 " --> pdb=" O VAL I 156 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA J 22 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN J 59 " --> pdb=" O ASN J 129 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN J 129 " --> pdb=" O ASN J 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 52 through 54 Processing sheet with id=AE5, first strand: chain 'K' and resid 22 through 23 removed outlier: 3.603A pdb=" N ALA K 22 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN K 59 " --> pdb=" O ASN K 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN K 129 " --> pdb=" O ASN K 59 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AE7, first strand: chain 'K' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU K 74 " --> pdb=" O THR K 153 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4246 1.34 - 1.46: 2492 1.46 - 1.57: 5395 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 12155 Sorted by residual: bond pdb=" N THR E 3 " pdb=" CA THR E 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.55e+00 bond pdb=" N THR I 3 " pdb=" CA THR I 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.54e+00 bond pdb=" N THR J 3 " pdb=" CA THR J 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.46e+00 bond pdb=" N THR G 3 " pdb=" CA THR G 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.46e+00 bond pdb=" N THR B 3 " pdb=" CA THR B 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.44e+00 ... (remaining 12150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 13942 1.27 - 2.55: 2434 2.55 - 3.82: 223 3.82 - 5.09: 0 5.09 - 6.36: 11 Bond angle restraints: 16610 Sorted by residual: angle pdb=" CA GLY J 75 " pdb=" C GLY J 75 " pdb=" N THR J 76 " ideal model delta sigma weight residual 115.34 117.69 -2.35 8.40e-01 1.42e+00 7.84e+00 angle pdb=" CA GLY A 75 " pdb=" C GLY A 75 " pdb=" N THR A 76 " ideal model delta sigma weight residual 115.34 117.66 -2.32 8.40e-01 1.42e+00 7.64e+00 angle pdb=" CA GLY E 75 " pdb=" C GLY E 75 " pdb=" N THR E 76 " ideal model delta sigma weight residual 115.34 117.66 -2.32 8.40e-01 1.42e+00 7.63e+00 angle pdb=" CA GLY B 75 " pdb=" C GLY B 75 " pdb=" N THR B 76 " ideal model delta sigma weight residual 115.34 117.65 -2.31 8.40e-01 1.42e+00 7.59e+00 angle pdb=" CA GLY C 75 " pdb=" C GLY C 75 " pdb=" N THR C 76 " ideal model delta sigma weight residual 115.34 117.65 -2.31 8.40e-01 1.42e+00 7.54e+00 ... (remaining 16605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 6721 14.78 - 29.55: 319 29.55 - 44.33: 22 44.33 - 59.10: 11 59.10 - 73.88: 11 Dihedral angle restraints: 7084 sinusoidal: 2277 harmonic: 4807 Sorted by residual: dihedral pdb=" CA SER H 50 " pdb=" C SER H 50 " pdb=" N ALA H 51 " pdb=" CA ALA H 51 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta harmonic sigma weight residual 180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA SER I 50 " pdb=" C SER I 50 " pdb=" N ALA I 51 " pdb=" CA ALA I 51 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1291 0.038 - 0.075: 553 0.075 - 0.113: 140 0.113 - 0.151: 84 0.151 - 0.189: 11 Chirality restraints: 2079 Sorted by residual: chirality pdb=" CA ILE E 56 " pdb=" N ILE E 56 " pdb=" C ILE E 56 " pdb=" CB ILE E 56 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA ILE K 56 " pdb=" N ILE K 56 " pdb=" C ILE K 56 " pdb=" CB ILE K 56 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA ILE B 56 " pdb=" N ILE B 56 " pdb=" C ILE B 56 " pdb=" CB ILE B 56 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 2076 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 144 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO K 145 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO K 145 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 145 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 144 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO I 145 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO I 145 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 145 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 144 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO C 145 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 145 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 145 " 0.029 5.00e-02 4.00e+02 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 806 2.70 - 3.25: 13039 3.25 - 3.80: 19384 3.80 - 4.35: 27058 4.35 - 4.90: 42511 Nonbonded interactions: 102798 Sorted by model distance: nonbonded pdb=" O VAL I 156 " pdb=" OG1 THR K 4 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR H 4 " pdb=" O VAL J 156 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR B 4 " pdb=" O VAL D 156 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR A 4 " pdb=" O VAL B 156 " model vdw 2.150 3.040 nonbonded pdb=" O VAL E 156 " pdb=" OG1 THR G 4 " model vdw 2.150 3.040 ... (remaining 102793 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.880 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12166 Z= 0.279 Angle : 0.924 6.365 16632 Z= 0.554 Chirality : 0.050 0.189 2079 Planarity : 0.004 0.051 2222 Dihedral : 9.181 73.877 3971 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: -4.46 (0.15), residues: 1694 helix: None (None), residues: 0 sheet: -2.78 (0.18), residues: 473 loop : -3.27 (0.14), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 106 TYR 0.005 0.002 TYR H 137 PHE 0.008 0.002 PHE E 73 HIS 0.006 0.003 HIS D 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.28 (12155) covalent geometry : angle 0.92340 / 0.55 (16610) SS BOND : bond 0.00441 / 0.26 ( 11) SS BOND : angle 1.27037 / 0.78 ( 22) hydrogen bonds : bond 0.26376 / 17.95 ( 296) hydrogen bonds : angle 15.77310 / 10.84 ( 690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.9035 (t) cc_final: 0.8469 (t) REVERT: B 58 LEU cc_start: 0.8473 (mt) cc_final: 0.8135 (mm) REVERT: D 86 LEU cc_start: 0.8140 (tp) cc_final: 0.7935 (tt) REVERT: F 58 LEU cc_start: 0.8442 (mt) cc_final: 0.7520 (mm) REVERT: G 58 LEU cc_start: 0.8507 (mt) cc_final: 0.7670 (mm) REVERT: H 58 LEU cc_start: 0.8158 (mt) cc_final: 0.7363 (mm) REVERT: H 151 ASP cc_start: 0.7944 (t0) cc_final: 0.7708 (p0) REVERT: I 16 VAL cc_start: 0.9021 (t) cc_final: 0.8818 (t) REVERT: J 86 LEU cc_start: 0.8059 (tp) cc_final: 0.7802 (tt) REVERT: K 31 THR cc_start: 0.8600 (m) cc_final: 0.8396 (p) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1061 time to fit residues: 53.6056 Evaluate side-chains 171 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 50.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.069923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.063070 restraints weight = 57893.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.064833 restraints weight = 35141.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066049 restraints weight = 23225.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.066904 restraints weight = 16178.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.067575 restraints weight = 11717.354| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12166 Z= 0.140 Angle : 0.588 5.922 16632 Z= 0.330 Chirality : 0.043 0.135 2079 Planarity : 0.004 0.041 2222 Dihedral : 5.511 19.202 1760 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.08 % Allowed : 0.98 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.18), residues: 1694 helix: -3.67 (0.44), residues: 66 sheet: -1.47 (0.22), residues: 451 loop : -2.48 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 136 TYR 0.013 0.003 TYR E 137 PHE 0.016 0.002 PHE B 118 HIS 0.003 0.001 HIS C 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (12155) covalent geometry : angle 0.58753 / 0.33 (16610) SS BOND : bond 0.00346 / 0.21 ( 11) SS BOND : angle 0.62677 / 0.40 ( 22) hydrogen bonds : bond 0.03795 / 2.53 ( 296) hydrogen bonds : angle 10.73074 / 7.31 ( 690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.8060 (tp30) cc_final: 0.7746 (tp30) REVERT: B 151 ASP cc_start: 0.8153 (t70) cc_final: 0.7925 (t70) REVERT: D 151 ASP cc_start: 0.7964 (t0) cc_final: 0.7748 (p0) REVERT: E 88 LEU cc_start: 0.8906 (mp) cc_final: 0.8457 (tt) REVERT: F 15 GLU cc_start: 0.8085 (tp30) cc_final: 0.7883 (tp30) REVERT: H 12 PHE cc_start: 0.8434 (m-80) cc_final: 0.7997 (m-10) REVERT: K 42 LEU cc_start: 0.8913 (mm) cc_final: 0.8631 (mt) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.0835 time to fit residues: 36.7904 Evaluate side-chains 158 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 159 optimal weight: 50.0000 chunk 141 optimal weight: 40.0000 chunk 114 optimal weight: 30.0000 chunk 33 optimal weight: 40.0000 chunk 96 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 50.0000 chunk 124 optimal weight: 8.9990 chunk 54 optimal weight: 50.0000 chunk 108 optimal weight: 50.0000 overall best weight: 17.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN J 36 GLN J 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.064834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.058130 restraints weight = 61350.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059853 restraints weight = 36755.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.061011 restraints weight = 24097.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061845 restraints weight = 16778.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.062489 restraints weight = 12181.120| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12166 Z= 0.254 Angle : 0.644 5.620 16632 Z= 0.359 Chirality : 0.043 0.149 2079 Planarity : 0.004 0.044 2222 Dihedral : 5.716 20.912 1760 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.18), residues: 1694 helix: -2.98 (0.64), residues: 66 sheet: -1.17 (0.21), residues: 451 loop : -2.09 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 136 TYR 0.016 0.003 TYR I 137 PHE 0.018 0.002 PHE H 118 HIS 0.008 0.003 HIS I 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.25 (12155) covalent geometry : angle 0.64361 / 0.36 (16610) SS BOND : bond 0.00575 / 0.35 ( 11) SS BOND : angle 1.09648 / 0.65 ( 22) hydrogen bonds : bond 0.04178 / 2.81 ( 296) hydrogen bonds : angle 10.53098 / 7.24 ( 690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7304 (m-30) cc_final: 0.6776 (m-30) REVERT: A 88 LEU cc_start: 0.8901 (mt) cc_final: 0.8653 (mt) REVERT: B 42 LEU cc_start: 0.9107 (mt) cc_final: 0.8816 (mt) REVERT: B 60 ASP cc_start: 0.7317 (m-30) cc_final: 0.6809 (m-30) REVERT: B 88 LEU cc_start: 0.8807 (mt) cc_final: 0.8533 (mt) REVERT: C 60 ASP cc_start: 0.7220 (m-30) cc_final: 0.6995 (m-30) REVERT: E 60 ASP cc_start: 0.7134 (m-30) cc_final: 0.6782 (m-30) REVERT: E 103 ILE cc_start: 0.8987 (tp) cc_final: 0.8753 (mm) REVERT: F 60 ASP cc_start: 0.7352 (m-30) cc_final: 0.6912 (m-30) REVERT: F 103 ILE cc_start: 0.8981 (tp) cc_final: 0.8764 (mm) REVERT: F 151 ASP cc_start: 0.8757 (t70) cc_final: 0.8241 (t0) REVERT: G 60 ASP cc_start: 0.7468 (m-30) cc_final: 0.7261 (m-30) REVERT: G 103 ILE cc_start: 0.8990 (tp) cc_final: 0.8770 (mm) REVERT: H 60 ASP cc_start: 0.7010 (m-30) cc_final: 0.6578 (m-30) REVERT: I 151 ASP cc_start: 0.8381 (t70) cc_final: 0.8093 (t0) REVERT: J 84 ASN cc_start: 0.8689 (m-40) cc_final: 0.8418 (p0) REVERT: K 154 PHE cc_start: 0.1948 (m-80) cc_final: -0.0141 (m-80) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.0904 time to fit residues: 32.2664 Evaluate side-chains 143 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 105 optimal weight: 70.0000 chunk 69 optimal weight: 40.0000 chunk 123 optimal weight: 0.8980 chunk 37 optimal weight: 50.0000 chunk 140 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 70 optimal weight: 40.0000 chunk 81 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 overall best weight: 7.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.067070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060362 restraints weight = 60071.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062049 restraints weight = 36469.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.063200 restraints weight = 24176.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064065 restraints weight = 16946.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064731 restraints weight = 12372.872| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12166 Z= 0.136 Angle : 0.538 5.701 16632 Z= 0.293 Chirality : 0.042 0.129 2079 Planarity : 0.004 0.040 2222 Dihedral : 4.841 16.689 1760 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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 are not related in a simple way. whole: -2.51 (0.18), residues: 1694 helix: -3.09 (0.58), residues: 66 sheet: -0.97 (0.23), residues: 440 loop : -1.98 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 136 TYR 0.010 0.002 TYR I 137 PHE 0.012 0.002 PHE J 12 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (12155) covalent geometry : angle 0.53662 / 0.29 (16610) SS BOND : bond 0.00211 / 0.13 ( 11) SS BOND : angle 1.14998 / 0.71 ( 22) hydrogen bonds : bond 0.03465 / 2.30 ( 296) hydrogen bonds : angle 9.80759 / 6.76 ( 690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8137 (tp30) cc_final: 0.7931 (tp30) REVERT: A 60 ASP cc_start: 0.7022 (m-30) cc_final: 0.6600 (m-30) REVERT: A 88 LEU cc_start: 0.8827 (mt) cc_final: 0.8580 (mt) REVERT: B 60 ASP cc_start: 0.7204 (m-30) cc_final: 0.6712 (m-30) REVERT: C 12 PHE cc_start: 0.8373 (m-80) cc_final: 0.7958 (m-10) REVERT: C 60 ASP cc_start: 0.7085 (m-30) cc_final: 0.6827 (m-30) REVERT: C 62 ASP cc_start: 0.8426 (t0) cc_final: 0.8211 (t0) REVERT: D 60 ASP cc_start: 0.6916 (m-30) cc_final: 0.6549 (m-30) REVERT: D 151 ASP cc_start: 0.8320 (t0) cc_final: 0.8045 (p0) REVERT: E 60 ASP cc_start: 0.6929 (m-30) cc_final: 0.6602 (m-30) REVERT: E 151 ASP cc_start: 0.8288 (t0) cc_final: 0.7974 (p0) REVERT: F 60 ASP cc_start: 0.7284 (m-30) cc_final: 0.6791 (m-30) REVERT: F 151 ASP cc_start: 0.8662 (t70) cc_final: 0.8202 (t0) REVERT: G 12 PHE cc_start: 0.8443 (m-80) cc_final: 0.8208 (m-10) REVERT: G 79 ASP cc_start: 0.7412 (m-30) cc_final: 0.7058 (p0) REVERT: G 88 LEU cc_start: 0.8897 (mt) cc_final: 0.8676 (mt) REVERT: G 151 ASP cc_start: 0.8475 (t70) cc_final: 0.8164 (t0) REVERT: H 12 PHE cc_start: 0.8182 (m-80) cc_final: 0.7831 (m-10) REVERT: H 60 ASP cc_start: 0.6832 (m-30) cc_final: 0.6488 (m-30) REVERT: H 84 ASN cc_start: 0.8660 (m-40) cc_final: 0.8449 (p0) REVERT: I 151 ASP cc_start: 0.8365 (t70) cc_final: 0.8101 (t0) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.0877 time to fit residues: 31.9655 Evaluate side-chains 145 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 31 optimal weight: 30.0000 chunk 151 optimal weight: 40.0000 chunk 45 optimal weight: 70.0000 chunk 9 optimal weight: 50.0000 chunk 114 optimal weight: 50.0000 chunk 95 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 40.0000 chunk 97 optimal weight: 40.0000 chunk 163 optimal weight: 20.0000 chunk 47 optimal weight: 50.0000 overall best weight: 21.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN K 30 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.063432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057096 restraints weight = 63510.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.058697 restraints weight = 38067.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.059805 restraints weight = 25052.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.060647 restraints weight = 17414.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.061308 restraints weight = 12589.731| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 12166 Z= 0.296 Angle : 0.677 7.637 16632 Z= 0.373 Chirality : 0.042 0.143 2079 Planarity : 0.004 0.041 2222 Dihedral : 5.855 21.308 1760 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 are not related in a simple way. whole: -2.52 (0.18), residues: 1694 helix: None (None), residues: 0 sheet: -1.11 (0.21), residues: 473 loop : -2.05 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 136 TYR 0.015 0.002 TYR G 137 PHE 0.017 0.002 PHE E 118 HIS 0.008 0.003 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.30 (12155) covalent geometry : angle 0.67471 / 0.37 (16610) SS BOND : bond 0.00458 / 0.28 ( 11) SS BOND : angle 1.68768 / 1.00 ( 22) hydrogen bonds : bond 0.04284 / 2.87 ( 296) hydrogen bonds : angle 10.34996 / 7.15 ( 690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8339 (m-10) cc_final: 0.8107 (m-80) REVERT: A 60 ASP cc_start: 0.7218 (m-30) cc_final: 0.6718 (m-30) REVERT: A 62 ASP cc_start: 0.8591 (t0) cc_final: 0.8348 (t0) REVERT: A 88 LEU cc_start: 0.8937 (mt) cc_final: 0.8388 (mt) REVERT: B 60 ASP cc_start: 0.7381 (m-30) cc_final: 0.6802 (m-30) REVERT: B 88 LEU cc_start: 0.8880 (mt) cc_final: 0.8570 (mt) REVERT: C 12 PHE cc_start: 0.8390 (m-80) cc_final: 0.7997 (m-10) REVERT: C 79 ASP cc_start: 0.7556 (m-30) cc_final: 0.6996 (p0) REVERT: D 12 PHE cc_start: 0.8322 (m-10) cc_final: 0.8061 (m-10) REVERT: D 60 ASP cc_start: 0.7418 (m-30) cc_final: 0.6894 (m-30) REVERT: D 62 ASP cc_start: 0.8410 (t0) cc_final: 0.8179 (t0) REVERT: E 60 ASP cc_start: 0.7213 (m-30) cc_final: 0.6857 (m-30) REVERT: F 60 ASP cc_start: 0.7511 (m-30) cc_final: 0.6799 (m-30) REVERT: F 151 ASP cc_start: 0.8675 (t70) cc_final: 0.8369 (t0) REVERT: G 12 PHE cc_start: 0.8387 (m-80) cc_final: 0.8064 (m-80) REVERT: G 13 LYS cc_start: 0.8443 (mmmt) cc_final: 0.8211 (mmmt) REVERT: G 15 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7134 (tp30) REVERT: G 34 LEU cc_start: 0.8824 (tt) cc_final: 0.8595 (tt) REVERT: G 60 ASP cc_start: 0.7512 (m-30) cc_final: 0.6883 (m-30) REVERT: G 88 LEU cc_start: 0.9128 (mt) cc_final: 0.8652 (mt) REVERT: H 60 ASP cc_start: 0.7142 (m-30) cc_final: 0.6690 (m-30) REVERT: I 62 ASP cc_start: 0.9003 (t0) cc_final: 0.8672 (t0) REVERT: K 12 PHE cc_start: 0.8250 (m-10) cc_final: 0.8038 (m-10) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0826 time to fit residues: 23.2639 Evaluate side-chains 129 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 20.0000 chunk 120 optimal weight: 40.0000 chunk 37 optimal weight: 50.0000 chunk 126 optimal weight: 20.0000 chunk 129 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 chunk 115 optimal weight: 50.0000 chunk 157 optimal weight: 50.0000 chunk 156 optimal weight: 30.0000 chunk 110 optimal weight: 5.9990 overall best weight: 17.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.064380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.058196 restraints weight = 61053.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.059914 restraints weight = 35691.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061046 restraints weight = 22895.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061862 restraints weight = 15601.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.062508 restraints weight = 11036.437| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12166 Z= 0.246 Angle : 0.636 6.928 16632 Z= 0.349 Chirality : 0.041 0.140 2079 Planarity : 0.004 0.039 2222 Dihedral : 5.520 20.654 1760 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.18), residues: 1694 helix: None (None), residues: 0 sheet: -1.18 (0.21), residues: 473 loop : -2.07 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 38 TYR 0.015 0.003 TYR B 158 PHE 0.017 0.002 PHE K 154 HIS 0.007 0.002 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.25 (12155) covalent geometry : angle 0.63332 / 0.35 (16610) SS BOND : bond 0.00374 / 0.22 ( 11) SS BOND : angle 1.58221 / 1.00 ( 22) hydrogen bonds : bond 0.04132 / 2.78 ( 296) hydrogen bonds : angle 9.90315 / 6.84 ( 690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7109 (m-30) cc_final: 0.6720 (m-30) REVERT: A 103 ILE cc_start: 0.9041 (tp) cc_final: 0.8797 (mm) REVERT: B 60 ASP cc_start: 0.7182 (m-30) cc_final: 0.6814 (m-30) REVERT: C 12 PHE cc_start: 0.8229 (m-80) cc_final: 0.7846 (m-10) REVERT: C 60 ASP cc_start: 0.7264 (m-30) cc_final: 0.7061 (m-30) REVERT: D 12 PHE cc_start: 0.8287 (m-10) cc_final: 0.8064 (m-10) REVERT: D 60 ASP cc_start: 0.7258 (m-30) cc_final: 0.6836 (m-30) REVERT: E 31 THR cc_start: 0.8231 (p) cc_final: 0.8025 (t) REVERT: F 60 ASP cc_start: 0.7450 (m-30) cc_final: 0.6849 (m-30) REVERT: F 103 ILE cc_start: 0.9020 (tp) cc_final: 0.8790 (mm) REVERT: F 151 ASP cc_start: 0.8557 (t70) cc_final: 0.8300 (t0) REVERT: G 34 LEU cc_start: 0.8910 (tt) cc_final: 0.8695 (tt) REVERT: G 60 ASP cc_start: 0.7137 (m-30) cc_final: 0.6789 (m-30) REVERT: H 60 ASP cc_start: 0.7079 (m-30) cc_final: 0.6724 (m-30) REVERT: I 62 ASP cc_start: 0.9014 (t0) cc_final: 0.8776 (t0) REVERT: J 62 ASP cc_start: 0.8312 (t0) cc_final: 0.8027 (t0) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0830 time to fit residues: 23.2838 Evaluate side-chains 132 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 41 optimal weight: 50.0000 chunk 120 optimal weight: 5.9990 chunk 24 optimal weight: 50.0000 chunk 159 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 15 optimal weight: 60.0000 chunk 3 optimal weight: 8.9990 chunk 53 optimal weight: 50.0000 chunk 123 optimal weight: 7.9990 chunk 74 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.059306 restraints weight = 59450.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.061055 restraints weight = 35083.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.062279 restraints weight = 22673.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.063175 restraints weight = 15452.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063829 restraints weight = 10957.154| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12166 Z= 0.135 Angle : 0.547 7.361 16632 Z= 0.292 Chirality : 0.041 0.129 2079 Planarity : 0.003 0.036 2222 Dihedral : 4.776 16.643 1760 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.19), residues: 1694 helix: None (None), residues: 0 sheet: -0.67 (0.22), residues: 451 loop : -1.75 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 106 TYR 0.016 0.002 TYR E 158 PHE 0.018 0.002 PHE K 154 HIS 0.003 0.001 HIS H 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (12155) covalent geometry : angle 0.54499 / 0.29 (16610) SS BOND : bond 0.00489 / 0.30 ( 11) SS BOND : angle 1.52312 / 0.96 ( 22) hydrogen bonds : bond 0.03541 / 2.36 ( 296) hydrogen bonds : angle 9.40235 / 6.50 ( 690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8885 (mmpt) cc_final: 0.8678 (mmmt) REVERT: A 60 ASP cc_start: 0.6974 (m-30) cc_final: 0.6622 (m-30) REVERT: A 88 LEU cc_start: 0.8871 (mt) cc_final: 0.8614 (mt) REVERT: B 60 ASP cc_start: 0.7154 (m-30) cc_final: 0.6819 (m-30) REVERT: B 84 ASN cc_start: 0.8604 (m-40) cc_final: 0.8266 (p0) REVERT: C 12 PHE cc_start: 0.8331 (m-80) cc_final: 0.7930 (m-10) REVERT: C 60 ASP cc_start: 0.7286 (m-30) cc_final: 0.7024 (m-30) REVERT: C 62 ASP cc_start: 0.8562 (t0) cc_final: 0.8294 (t0) REVERT: C 79 ASP cc_start: 0.7510 (m-30) cc_final: 0.7054 (p0) REVERT: D 12 PHE cc_start: 0.8308 (m-10) cc_final: 0.7975 (m-10) REVERT: E 151 ASP cc_start: 0.8403 (t70) cc_final: 0.8022 (t0) REVERT: F 12 PHE cc_start: 0.7881 (m-80) cc_final: 0.7576 (m-80) REVERT: F 151 ASP cc_start: 0.8543 (t70) cc_final: 0.8280 (t0) REVERT: G 60 ASP cc_start: 0.7259 (m-30) cc_final: 0.6901 (m-30) REVERT: G 151 ASP cc_start: 0.8432 (t0) cc_final: 0.8199 (p0) REVERT: H 12 PHE cc_start: 0.8193 (m-80) cc_final: 0.7852 (m-10) REVERT: H 60 ASP cc_start: 0.6960 (m-30) cc_final: 0.6608 (m-30) REVERT: I 12 PHE cc_start: 0.8420 (m-80) cc_final: 0.8152 (m-10) REVERT: K 12 PHE cc_start: 0.8315 (m-80) cc_final: 0.8051 (m-10) REVERT: K 88 LEU cc_start: 0.8791 (mt) cc_final: 0.8571 (mt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.0858 time to fit residues: 27.1952 Evaluate side-chains 156 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 51 optimal weight: 40.0000 chunk 118 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 chunk 49 optimal weight: 50.0000 chunk 162 optimal weight: 30.0000 chunk 99 optimal weight: 50.0000 chunk 157 optimal weight: 7.9990 chunk 54 optimal weight: 50.0000 chunk 147 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 overall best weight: 17.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058211 restraints weight = 60796.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.059865 restraints weight = 35909.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.060991 restraints weight = 23309.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061785 restraints weight = 16024.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062339 restraints weight = 11474.245| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 12166 Z= 0.244 Angle : 0.627 6.851 16632 Z= 0.342 Chirality : 0.041 0.158 2079 Planarity : 0.003 0.034 2222 Dihedral : 5.423 20.746 1760 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.18), residues: 1694 helix: None (None), residues: 0 sheet: -1.04 (0.21), residues: 495 loop : -1.96 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.013 0.003 TYR E 158 PHE 0.019 0.002 PHE G 118 HIS 0.007 0.002 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.24 (12155) covalent geometry : angle 0.62426 / 0.34 (16610) SS BOND : bond 0.00618 / 0.40 ( 11) SS BOND : angle 1.64885 / 1.05 ( 22) hydrogen bonds : bond 0.04017 / 2.71 ( 296) hydrogen bonds : angle 9.82847 / 6.81 ( 690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8307 (m-10) cc_final: 0.7996 (m-10) REVERT: A 13 LYS cc_start: 0.9007 (mmpt) cc_final: 0.8749 (mmmt) REVERT: A 88 LEU cc_start: 0.8932 (mt) cc_final: 0.8663 (mt) REVERT: B 60 ASP cc_start: 0.7342 (m-30) cc_final: 0.6974 (m-30) REVERT: B 62 ASP cc_start: 0.8616 (t0) cc_final: 0.8406 (t0) REVERT: B 151 ASP cc_start: 0.8541 (t70) cc_final: 0.8170 (t0) REVERT: C 60 ASP cc_start: 0.7406 (m-30) cc_final: 0.7165 (m-30) REVERT: D 12 PHE cc_start: 0.8333 (m-10) cc_final: 0.8119 (m-10) REVERT: D 60 ASP cc_start: 0.7116 (m-30) cc_final: 0.6755 (m-30) REVERT: E 151 ASP cc_start: 0.8508 (t70) cc_final: 0.8241 (t0) REVERT: F 60 ASP cc_start: 0.7084 (m-30) cc_final: 0.6765 (m-30) REVERT: F 103 ILE cc_start: 0.9023 (tp) cc_final: 0.8805 (mm) REVERT: F 151 ASP cc_start: 0.8579 (t70) cc_final: 0.8328 (t0) REVERT: G 60 ASP cc_start: 0.7229 (m-30) cc_final: 0.6889 (m-30) REVERT: H 60 ASP cc_start: 0.7182 (m-30) cc_final: 0.6834 (m-30) REVERT: I 62 ASP cc_start: 0.9085 (t0) cc_final: 0.8816 (t0) REVERT: I 84 ASN cc_start: 0.8931 (m-40) cc_final: 0.8322 (p0) REVERT: J 154 PHE cc_start: 0.7724 (t80) cc_final: 0.7498 (t80) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0845 time to fit residues: 24.1860 Evaluate side-chains 139 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 154 optimal weight: 10.0000 chunk 124 optimal weight: 50.0000 chunk 128 optimal weight: 50.0000 chunk 92 optimal weight: 50.0000 chunk 71 optimal weight: 50.0000 chunk 64 optimal weight: 50.0000 chunk 27 optimal weight: 50.0000 chunk 69 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 23 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 overall best weight: 24.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.062751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.056799 restraints weight = 62172.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058401 restraints weight = 36247.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.059489 restraints weight = 23289.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060283 restraints weight = 15873.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060794 restraints weight = 11313.523| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.7041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 12166 Z= 0.328 Angle : 0.728 7.940 16632 Z= 0.401 Chirality : 0.043 0.185 2079 Planarity : 0.004 0.034 2222 Dihedral : 6.218 26.370 1760 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.08 % Allowed : 1.39 % Favored : 98.53 % 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 are not related in a simple way. whole: -2.73 (0.18), residues: 1694 helix: None (None), residues: 0 sheet: -1.35 (0.20), residues: 495 loop : -2.15 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 38 TYR 0.016 0.003 TYR G 137 PHE 0.025 0.003 PHE F 154 HIS 0.009 0.003 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.33 (12155) covalent geometry : angle 0.72516 / 0.40 (16610) SS BOND : bond 0.00667 / 0.40 ( 11) SS BOND : angle 1.78316 / 1.15 ( 22) hydrogen bonds : bond 0.04637 / 3.14 ( 296) hydrogen bonds : angle 10.38228 / 7.21 ( 690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8820 (mmpt) cc_final: 0.8558 (mmmt) REVERT: A 62 ASP cc_start: 0.8513 (t0) cc_final: 0.8304 (t0) REVERT: A 88 LEU cc_start: 0.8907 (mt) cc_final: 0.8615 (mt) REVERT: B 60 ASP cc_start: 0.7318 (m-30) cc_final: 0.7020 (m-30) REVERT: B 62 ASP cc_start: 0.8685 (t0) cc_final: 0.8385 (t0) REVERT: B 151 ASP cc_start: 0.8546 (t70) cc_final: 0.8290 (t0) REVERT: C 60 ASP cc_start: 0.7616 (m-30) cc_final: 0.7348 (m-30) REVERT: D 12 PHE cc_start: 0.8365 (m-10) cc_final: 0.8158 (m-10) REVERT: D 60 ASP cc_start: 0.7323 (m-30) cc_final: 0.6914 (m-30) REVERT: D 62 ASP cc_start: 0.8337 (t0) cc_final: 0.8079 (t0) REVERT: D 88 LEU cc_start: 0.9027 (mt) cc_final: 0.8783 (mt) REVERT: D 154 PHE cc_start: 0.7754 (t80) cc_final: 0.7494 (t80) REVERT: E 151 ASP cc_start: 0.8524 (t70) cc_final: 0.8150 (t0) REVERT: F 60 ASP cc_start: 0.7209 (m-30) cc_final: 0.6993 (m-30) REVERT: F 62 ASP cc_start: 0.8168 (t0) cc_final: 0.7926 (t0) REVERT: F 103 ILE cc_start: 0.9024 (tp) cc_final: 0.8770 (mm) REVERT: F 151 ASP cc_start: 0.8491 (t70) cc_final: 0.8255 (t0) REVERT: G 60 ASP cc_start: 0.7303 (m-30) cc_final: 0.6863 (m-30) REVERT: H 60 ASP cc_start: 0.7419 (m-30) cc_final: 0.7019 (m-30) REVERT: I 154 PHE cc_start: 0.7661 (t80) cc_final: 0.7460 (t80) REVERT: J 154 PHE cc_start: 0.7876 (t80) cc_final: 0.7459 (t80) outliers start: 1 outliers final: 1 residues processed: 163 average time/residue: 0.0821 time to fit residues: 21.0176 Evaluate side-chains 136 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 42 optimal weight: 30.0000 chunk 99 optimal weight: 50.0000 chunk 61 optimal weight: 50.0000 chunk 19 optimal weight: 40.0000 chunk 134 optimal weight: 40.0000 chunk 153 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 158 optimal weight: 40.0000 chunk 97 optimal weight: 40.0000 chunk 151 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 overall best weight: 13.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN I 36 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.064662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058350 restraints weight = 60664.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060017 restraints weight = 35646.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061158 restraints weight = 23089.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.062007 restraints weight = 15838.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.062635 restraints weight = 11302.963| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12166 Z= 0.207 Angle : 0.632 6.998 16632 Z= 0.340 Chirality : 0.042 0.161 2079 Planarity : 0.003 0.036 2222 Dihedral : 5.636 21.803 1760 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.08 % Allowed : 0.08 % Favored : 99.84 % 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 are not related in a simple way. whole: -2.53 (0.18), residues: 1694 helix: None (None), residues: 0 sheet: -1.24 (0.21), residues: 495 loop : -2.00 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 38 TYR 0.013 0.002 TYR E 137 PHE 0.021 0.003 PHE F 154 HIS 0.005 0.002 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (12155) covalent geometry : angle 0.62946 / 0.34 (16610) SS BOND : bond 0.00500 / 0.30 ( 11) SS BOND : angle 1.64861 / 1.06 ( 22) hydrogen bonds : bond 0.04006 / 2.70 ( 296) hydrogen bonds : angle 9.96055 / 6.92 ( 690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 ASP cc_start: 0.7383 (m-30) cc_final: 0.7078 (m-30) REVERT: B 62 ASP cc_start: 0.8692 (t0) cc_final: 0.8485 (t0) REVERT: B 151 ASP cc_start: 0.8532 (t70) cc_final: 0.8153 (t0) REVERT: C 60 ASP cc_start: 0.7485 (m-30) cc_final: 0.7024 (m-30) REVERT: D 60 ASP cc_start: 0.7371 (m-30) cc_final: 0.6932 (m-30) REVERT: D 88 LEU cc_start: 0.9022 (mt) cc_final: 0.8787 (mt) REVERT: F 60 ASP cc_start: 0.7273 (m-30) cc_final: 0.7020 (m-30) REVERT: F 103 ILE cc_start: 0.9027 (tp) cc_final: 0.8805 (mm) REVERT: F 151 ASP cc_start: 0.8562 (t70) cc_final: 0.8278 (t0) REVERT: G 60 ASP cc_start: 0.7373 (m-30) cc_final: 0.6868 (m-30) REVERT: H 60 ASP cc_start: 0.7252 (m-30) cc_final: 0.6839 (m-30) REVERT: I 13 LYS cc_start: 0.8587 (mppt) cc_final: 0.8256 (mptt) REVERT: I 84 ASN cc_start: 0.8756 (m-40) cc_final: 0.8350 (p0) REVERT: J 151 ASP cc_start: 0.8513 (t0) cc_final: 0.8167 (p0) REVERT: J 154 PHE cc_start: 0.7777 (t80) cc_final: 0.7455 (t80) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.0836 time to fit residues: 21.5941 Evaluate side-chains 143 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 49 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 chunk 130 optimal weight: 40.0000 chunk 145 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 116 optimal weight: 40.0000 chunk 92 optimal weight: 6.9990 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.065741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.059509 restraints weight = 59687.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061188 restraints weight = 34825.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.062353 restraints weight = 22375.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063190 restraints weight = 15240.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.063805 restraints weight = 10779.893| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.7089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12166 Z= 0.159 Angle : 0.597 7.248 16632 Z= 0.317 Chirality : 0.042 0.144 2079 Planarity : 0.003 0.036 2222 Dihedral : 5.268 19.025 1760 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.67 % 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 are not related in a simple way. whole: -2.46 (0.18), residues: 1694 helix: -2.03 (0.71), residues: 66 sheet: -1.09 (0.21), residues: 495 loop : -1.96 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 38 TYR 0.012 0.002 TYR F 158 PHE 0.020 0.002 PHE F 154 HIS 0.005 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (12155) covalent geometry : angle 0.59429 / 0.32 (16610) SS BOND : bond 0.00405 / 0.24 ( 11) SS BOND : angle 1.54686 / 0.99 ( 22) hydrogen bonds : bond 0.03752 / 2.54 ( 296) hydrogen bonds : angle 9.52609 / 6.59 ( 690) =============================================================================== Job complete usr+sys time: 1497.79 seconds wall clock time: 27 minutes 11.42 seconds (1631.42 seconds total)