Starting phenix.real_space_refine on Tue Jun 10 14:59:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c53_7342/06_2025/6c53_7342.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c53_7342/06_2025/6c53_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6c53_7342/06_2025/6c53_7342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c53_7342/06_2025/6c53_7342.map" model { file = "/net/cci-nas-00/data/ceres_data/6c53_7342/06_2025/6c53_7342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c53_7342/06_2025/6c53_7342.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J Time building chain proxies: 3.75, per 1000 atoms: 0.31 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 C 21 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 61 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 61 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 61 " distance=2.03 Simple disulfide: pdb=" SG CYS K 21 " - pdb=" SG CYS K 61 " distance=2.03 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 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: 2.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.90 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: 3.45 Time building geometry restraints manager: 3.49 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' } 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.100 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (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 HIS 0.006 0.003 HIS D 11 PHE 0.008 0.002 PHE E 73 TYR 0.005 0.002 TYR H 137 ARG 0.002 0.001 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.26376 ( 296) hydrogen bonds : angle 15.77310 ( 690) SS BOND : bond 0.00441 ( 11) SS BOND : angle 1.27037 ( 22) covalent geometry : bond 0.00598 (12155) covalent geometry : angle 0.92340 (16610) *********************** 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 : 1.295 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: 0.8136 (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: 0.7362 (mm) REVERT: H 151 ASP cc_start: 0.7945 (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: 0.8601 (m) cc_final: 0.8396 (p) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2433 time to fit residues: 121.1860 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 : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 50.0000 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 84 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 0.2980 chunk 50 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 149 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.071101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.064248 restraints weight = 57122.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066021 restraints weight = 34673.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.067231 restraints weight = 22882.423| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12166 Z= 0.125 Angle : 0.588 6.050 16632 Z= 0.328 Chirality : 0.044 0.138 2079 Planarity : 0.004 0.042 2222 Dihedral : 5.476 19.202 1760 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.08 % Allowed : 0.90 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.18), residues: 1694 helix: -3.87 (0.39), residues: 66 sheet: -1.54 (0.22), residues: 451 loop : -2.48 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 82 PHE 0.015 0.002 PHE B 118 TYR 0.012 0.003 TYR E 137 ARG 0.005 0.001 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 296) hydrogen bonds : angle 10.78575 ( 690) SS BOND : bond 0.00293 ( 11) SS BOND : angle 0.65236 ( 22) covalent geometry : bond 0.00268 (12155) covalent geometry : angle 0.58775 (16610) *********************** 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 294 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 SER cc_start: 0.8423 (t) cc_final: 0.8206 (p) REVERT: B 15 GLU cc_start: 0.8026 (tp30) cc_final: 0.7640 (tp30) REVERT: B 151 ASP cc_start: 0.8342 (t70) cc_final: 0.8109 (t0) REVERT: C 151 ASP cc_start: 0.8130 (t70) cc_final: 0.7858 (t70) REVERT: D 151 ASP cc_start: 0.7986 (t0) cc_final: 0.7761 (p0) REVERT: E 88 LEU cc_start: 0.8882 (mp) cc_final: 0.8461 (tt) REVERT: E 151 ASP cc_start: 0.8383 (t0) cc_final: 0.7817 (p0) REVERT: F 15 GLU cc_start: 0.8077 (tp30) cc_final: 0.7840 (tp30) REVERT: F 62 ASP cc_start: 0.8124 (t0) cc_final: 0.7898 (p0) REVERT: G 79 ASP cc_start: 0.7521 (m-30) cc_final: 0.7130 (p0) REVERT: H 12 PHE cc_start: 0.8424 (m-80) cc_final: 0.8171 (m-80) REVERT: J 62 ASP cc_start: 0.7941 (t0) cc_final: 0.7686 (p0) REVERT: K 42 LEU cc_start: 0.8892 (mm) cc_final: 0.8584 (mt) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.1912 time to fit residues: 86.0946 Evaluate side-chains 165 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 70.0000 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 128 optimal weight: 50.0000 chunk 18 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 chunk 2 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN C 30 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.067906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061127 restraints weight = 59694.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062861 restraints weight = 35942.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.064042 restraints weight = 23643.552| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12166 Z= 0.153 Angle : 0.552 4.953 16632 Z= 0.305 Chirality : 0.042 0.138 2079 Planarity : 0.004 0.039 2222 Dihedral : 4.975 16.854 1760 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.19), residues: 1694 helix: -3.53 (0.49), residues: 66 sheet: -0.80 (0.22), residues: 429 loop : -1.98 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 82 PHE 0.013 0.002 PHE I 118 TYR 0.013 0.003 TYR I 137 ARG 0.003 0.001 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 296) hydrogen bonds : angle 9.99409 ( 690) SS BOND : bond 0.00356 ( 11) SS BOND : angle 0.87572 ( 22) covalent geometry : bond 0.00325 (12155) covalent geometry : angle 0.55161 (16610) *********************** 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 263 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7313 (m-30) cc_final: 0.6748 (m-30) REVERT: B 60 ASP cc_start: 0.7240 (m-30) cc_final: 0.6872 (m-30) REVERT: B 151 ASP cc_start: 0.8265 (t70) cc_final: 0.7931 (t0) REVERT: C 60 ASP cc_start: 0.7009 (m-30) cc_final: 0.6776 (m-30) REVERT: D 42 LEU cc_start: 0.9084 (mt) cc_final: 0.8853 (mt) REVERT: D 62 ASP cc_start: 0.8103 (t0) cc_final: 0.7704 (p0) REVERT: D 65 VAL cc_start: 0.8751 (t) cc_final: 0.8550 (t) REVERT: E 60 ASP cc_start: 0.7024 (m-30) cc_final: 0.6564 (m-30) REVERT: F 60 ASP cc_start: 0.7131 (m-30) cc_final: 0.6593 (m-30) REVERT: F 151 ASP cc_start: 0.8664 (t70) cc_final: 0.8130 (t0) REVERT: G 60 ASP cc_start: 0.7178 (m-30) cc_final: 0.6708 (m-30) REVERT: H 31 THR cc_start: 0.8678 (m) cc_final: 0.8459 (p) REVERT: H 60 ASP cc_start: 0.6874 (m-30) cc_final: 0.6462 (m-30) REVERT: I 151 ASP cc_start: 0.8224 (t70) cc_final: 0.8017 (t0) REVERT: J 67 SER cc_start: 0.8612 (p) cc_final: 0.8096 (m) REVERT: K 42 LEU cc_start: 0.9009 (mm) cc_final: 0.8761 (mt) REVERT: K 62 ASP cc_start: 0.8293 (t0) cc_final: 0.8068 (p0) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2403 time to fit residues: 95.0873 Evaluate side-chains 149 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 108 optimal weight: 40.0000 chunk 129 optimal weight: 50.0000 chunk 25 optimal weight: 50.0000 chunk 106 optimal weight: 7.9990 chunk 22 optimal weight: 50.0000 chunk 39 optimal weight: 50.0000 chunk 51 optimal weight: 50.0000 chunk 6 optimal weight: 10.0000 chunk 122 optimal weight: 50.0000 chunk 14 optimal weight: 50.0000 chunk 78 optimal weight: 10.0000 overall best weight: 23.5998 ------------------------------------------------------------------------------- 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** ** 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** G 36 GLN H 36 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.062071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055832 restraints weight = 63198.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.057396 restraints weight = 38104.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.058484 restraints weight = 25139.541| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 12166 Z= 0.333 Angle : 0.725 8.269 16632 Z= 0.402 Chirality : 0.043 0.172 2079 Planarity : 0.004 0.040 2222 Dihedral : 6.150 22.239 1760 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.16 % Allowed : 3.36 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.18), residues: 1694 helix: None (None), residues: 0 sheet: -1.01 (0.21), residues: 473 loop : -2.17 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS E 11 PHE 0.017 0.003 PHE C 133 TYR 0.016 0.003 TYR E 137 ARG 0.005 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 296) hydrogen bonds : angle 10.82016 ( 690) SS BOND : bond 0.00570 ( 11) SS BOND : angle 1.31552 ( 22) covalent geometry : bond 0.00685 (12155) covalent geometry : angle 0.72364 (16610) *********************** 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 191 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7134 (m-30) cc_final: 0.6653 (m-30) REVERT: A 62 ASP cc_start: 0.8395 (t0) cc_final: 0.8184 (t0) REVERT: B 60 ASP cc_start: 0.7349 (m-30) cc_final: 0.6733 (m-30) REVERT: B 62 ASP cc_start: 0.8667 (t0) cc_final: 0.8449 (t0) REVERT: C 60 ASP cc_start: 0.7352 (m-30) cc_final: 0.7020 (m-30) REVERT: C 62 ASP cc_start: 0.8311 (t0) cc_final: 0.8027 (t0) REVERT: C 79 ASP cc_start: 0.7612 (m-30) cc_final: 0.7006 (p0) REVERT: D 12 PHE cc_start: 0.8344 (m-10) cc_final: 0.8101 (m-10) REVERT: D 60 ASP cc_start: 0.7211 (m-30) cc_final: 0.7008 (m-30) REVERT: D 62 ASP cc_start: 0.8408 (t0) cc_final: 0.8085 (t0) REVERT: F 60 ASP cc_start: 0.7518 (m-30) cc_final: 0.6874 (m-30) REVERT: F 151 ASP cc_start: 0.8817 (t70) cc_final: 0.8422 (t0) REVERT: G 12 PHE cc_start: 0.8185 (m-10) cc_final: 0.7946 (m-80) REVERT: G 88 LEU cc_start: 0.9134 (mt) cc_final: 0.8895 (mt) REVERT: H 60 ASP cc_start: 0.7163 (m-30) cc_final: 0.6721 (m-30) REVERT: I 151 ASP cc_start: 0.8390 (t70) cc_final: 0.8122 (t0) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.2129 time to fit residues: 61.5296 Evaluate side-chains 127 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 137 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 30.0000 chunk 27 optimal weight: 50.0000 chunk 29 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 chunk 161 optimal weight: 40.0000 chunk 136 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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** ** C 36 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** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 = 0.3344 r_free = 0.3344 target = 0.065400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.058792 restraints weight = 60068.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060474 restraints weight = 36122.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061631 restraints weight = 23691.871| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12166 Z= 0.153 Angle : 0.552 6.173 16632 Z= 0.302 Chirality : 0.042 0.147 2079 Planarity : 0.004 0.041 2222 Dihedral : 4.994 17.789 1760 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.18), residues: 1694 helix: None (None), residues: 0 sheet: -1.08 (0.22), residues: 484 loop : -1.99 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 11 PHE 0.015 0.002 PHE H 118 TYR 0.011 0.002 TYR K 158 ARG 0.002 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 296) hydrogen bonds : angle 9.76211 ( 690) SS BOND : bond 0.00267 ( 11) SS BOND : angle 1.49782 ( 22) covalent geometry : bond 0.00321 (12155) covalent geometry : angle 0.54982 (16610) *********************** 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 230 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7150 (m-30) cc_final: 0.6646 (m-30) REVERT: B 60 ASP cc_start: 0.7383 (m-30) cc_final: 0.6763 (m-30) REVERT: B 84 ASN cc_start: 0.8530 (m-40) cc_final: 0.8321 (p0) REVERT: C 12 PHE cc_start: 0.8214 (m-80) cc_final: 0.7708 (m-10) REVERT: C 60 ASP cc_start: 0.7299 (m-30) cc_final: 0.6989 (m-30) REVERT: C 62 ASP cc_start: 0.8411 (t0) cc_final: 0.8164 (t0) REVERT: D 60 ASP cc_start: 0.7064 (m-30) cc_final: 0.6751 (m-30) REVERT: D 84 ASN cc_start: 0.8671 (m-40) cc_final: 0.8312 (p0) REVERT: E 60 ASP cc_start: 0.7091 (m-30) cc_final: 0.6816 (m-30) REVERT: F 12 PHE cc_start: 0.8022 (m-80) cc_final: 0.7748 (m-80) REVERT: F 60 ASP cc_start: 0.7486 (m-30) cc_final: 0.6938 (m-30) REVERT: F 151 ASP cc_start: 0.8738 (t70) cc_final: 0.8417 (t0) REVERT: G 15 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7175 (tp30) REVERT: G 151 ASP cc_start: 0.8651 (t70) cc_final: 0.8187 (p0) REVERT: H 60 ASP cc_start: 0.6988 (m-30) cc_final: 0.6625 (m-30) REVERT: H 84 ASN cc_start: 0.8728 (m-40) cc_final: 0.8333 (p0) REVERT: I 151 ASP cc_start: 0.8442 (t70) cc_final: 0.8222 (t0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1908 time to fit residues: 67.3538 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 : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 57 optimal weight: 30.0000 chunk 107 optimal weight: 50.0000 chunk 116 optimal weight: 50.0000 chunk 59 optimal weight: 8.9990 chunk 112 optimal weight: 50.0000 chunk 49 optimal weight: 50.0000 chunk 79 optimal weight: 20.0000 chunk 131 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 134 optimal weight: 40.0000 chunk 117 optimal weight: 40.0000 overall best weight: 13.9394 ------------------------------------------------------------------------------- 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** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.059581 restraints weight = 59282.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061311 restraints weight = 34710.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062446 restraints weight = 22252.143| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12166 Z= 0.208 Angle : 0.582 6.275 16632 Z= 0.322 Chirality : 0.041 0.135 2079 Planarity : 0.004 0.039 2222 Dihedral : 5.150 18.630 1760 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.18), residues: 1694 helix: None (None), residues: 0 sheet: -1.04 (0.21), residues: 484 loop : -1.94 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 11 PHE 0.013 0.002 PHE H 118 TYR 0.011 0.002 TYR G 137 ARG 0.004 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 296) hydrogen bonds : angle 9.78830 ( 690) SS BOND : bond 0.00313 ( 11) SS BOND : angle 1.60051 ( 22) covalent geometry : bond 0.00433 (12155) covalent geometry : angle 0.57944 (16610) *********************** 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 184 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7178 (m-30) cc_final: 0.6763 (m-30) REVERT: A 151 ASP cc_start: 0.8319 (t0) cc_final: 0.8110 (p0) REVERT: B 60 ASP cc_start: 0.7418 (m-30) cc_final: 0.6865 (m-30) REVERT: B 62 ASP cc_start: 0.8826 (t0) cc_final: 0.8586 (t0) REVERT: C 60 ASP cc_start: 0.7326 (m-30) cc_final: 0.7026 (m-30) REVERT: C 79 ASP cc_start: 0.7514 (m-30) cc_final: 0.7072 (p0) REVERT: C 151 ASP cc_start: 0.8471 (t70) cc_final: 0.8248 (t0) REVERT: D 12 PHE cc_start: 0.8366 (m-10) cc_final: 0.8078 (m-10) REVERT: D 62 ASP cc_start: 0.8476 (t0) cc_final: 0.8224 (t0) REVERT: E 60 ASP cc_start: 0.7159 (m-30) cc_final: 0.6848 (m-30) REVERT: F 60 ASP cc_start: 0.7431 (m-30) cc_final: 0.6734 (m-30) REVERT: F 88 LEU cc_start: 0.9101 (mt) cc_final: 0.8886 (mt) REVERT: F 151 ASP cc_start: 0.8653 (t70) cc_final: 0.8364 (t0) REVERT: G 88 LEU cc_start: 0.8809 (mt) cc_final: 0.8559 (mt) REVERT: G 151 ASP cc_start: 0.8689 (t70) cc_final: 0.8184 (p0) REVERT: H 60 ASP cc_start: 0.7055 (m-30) cc_final: 0.6653 (m-30) REVERT: I 62 ASP cc_start: 0.9044 (t0) cc_final: 0.8829 (t0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2300 time to fit residues: 64.7339 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 : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 50.0000 chunk 57 optimal weight: 10.0000 chunk 88 optimal weight: 50.0000 chunk 17 optimal weight: 40.0000 chunk 117 optimal weight: 30.0000 chunk 45 optimal weight: 60.0000 chunk 33 optimal weight: 8.9990 chunk 141 optimal weight: 30.0000 chunk 122 optimal weight: 30.0000 chunk 15 optimal weight: 60.0000 chunk 58 optimal weight: 10.0000 overall best weight: 17.7998 ------------------------------------------------------------------------------- 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** ** B 36 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 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** 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 = 0.064588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058247 restraints weight = 59505.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.059994 restraints weight = 34642.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061153 restraints weight = 22221.580| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12166 Z= 0.254 Angle : 0.632 7.102 16632 Z= 0.350 Chirality : 0.042 0.153 2079 Planarity : 0.004 0.036 2222 Dihedral : 5.548 20.213 1760 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.18), residues: 1694 helix: None (None), residues: 0 sheet: -1.14 (0.21), residues: 495 loop : -1.99 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 11 PHE 0.015 0.002 PHE H 118 TYR 0.015 0.003 TYR B 158 ARG 0.004 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 296) hydrogen bonds : angle 9.94784 ( 690) SS BOND : bond 0.00493 ( 11) SS BOND : angle 1.46506 ( 22) covalent geometry : bond 0.00524 (12155) covalent geometry : angle 0.63036 (16610) *********************** 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 177 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7251 (m-30) cc_final: 0.6855 (m-30) REVERT: A 103 ILE cc_start: 0.9111 (tp) cc_final: 0.8882 (mm) REVERT: A 154 PHE cc_start: 0.7673 (t80) cc_final: 0.7392 (t80) REVERT: B 60 ASP cc_start: 0.7412 (m-30) cc_final: 0.6975 (m-30) REVERT: C 79 ASP cc_start: 0.7597 (m-30) cc_final: 0.7041 (p0) REVERT: D 12 PHE cc_start: 0.8407 (m-10) cc_final: 0.8027 (m-10) REVERT: D 62 ASP cc_start: 0.8571 (t0) cc_final: 0.8183 (t0) REVERT: E 60 ASP cc_start: 0.7256 (m-30) cc_final: 0.6953 (m-30) REVERT: F 60 ASP cc_start: 0.7392 (m-30) cc_final: 0.6809 (m-30) REVERT: F 62 ASP cc_start: 0.8332 (t0) cc_final: 0.8106 (t0) REVERT: F 151 ASP cc_start: 0.8604 (t70) cc_final: 0.8349 (t0) REVERT: G 151 ASP cc_start: 0.8530 (t70) cc_final: 0.8126 (p0) REVERT: H 60 ASP cc_start: 0.7263 (m-30) cc_final: 0.6866 (m-30) REVERT: I 62 ASP cc_start: 0.9060 (t0) cc_final: 0.8843 (t0) REVERT: J 62 ASP cc_start: 0.8228 (t0) cc_final: 0.7932 (t0) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2175 time to fit residues: 59.7907 Evaluate side-chains 134 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 79 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 30.0000 chunk 156 optimal weight: 0.8980 chunk 132 optimal weight: 0.0570 chunk 128 optimal weight: 30.0000 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 50.0000 chunk 102 optimal weight: 50.0000 chunk 154 optimal weight: 8.9990 overall best weight: 5.1904 ------------------------------------------------------------------------------- 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** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 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 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.067701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061049 restraints weight = 58664.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.062841 restraints weight = 34258.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.064062 restraints weight = 22131.616| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.6662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12166 Z= 0.118 Angle : 0.549 6.414 16632 Z= 0.293 Chirality : 0.041 0.128 2079 Planarity : 0.003 0.035 2222 Dihedral : 4.732 17.970 1760 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.08 % Allowed : 1.56 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.19), residues: 1694 helix: -2.56 (0.63), residues: 66 sheet: -0.98 (0.22), residues: 484 loop : -1.82 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 11 PHE 0.022 0.002 PHE G 118 TYR 0.013 0.002 TYR H 158 ARG 0.002 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 296) hydrogen bonds : angle 9.28866 ( 690) SS BOND : bond 0.00335 ( 11) SS BOND : angle 1.50998 ( 22) covalent geometry : bond 0.00256 (12155) covalent geometry : angle 0.54642 (16610) *********************** 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 203 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7109 (m-30) cc_final: 0.6693 (m-30) REVERT: B 60 ASP cc_start: 0.7280 (m-30) cc_final: 0.6838 (m-30) REVERT: B 62 ASP cc_start: 0.8774 (t0) cc_final: 0.8562 (t0) REVERT: C 60 ASP cc_start: 0.7314 (m-30) cc_final: 0.6770 (m-30) REVERT: C 62 ASP cc_start: 0.8692 (t0) cc_final: 0.8421 (t0) REVERT: D 12 PHE cc_start: 0.8446 (m-10) cc_final: 0.7934 (m-10) REVERT: D 62 ASP cc_start: 0.8629 (t0) cc_final: 0.8356 (t0) REVERT: E 60 ASP cc_start: 0.7186 (m-30) cc_final: 0.6908 (m-30) REVERT: E 151 ASP cc_start: 0.8650 (t0) cc_final: 0.8029 (p0) REVERT: F 89 GLN cc_start: 0.8270 (mp10) cc_final: 0.7882 (tp-100) REVERT: F 151 ASP cc_start: 0.8524 (t70) cc_final: 0.7920 (p0) REVERT: G 84 ASN cc_start: 0.8910 (m-40) cc_final: 0.8259 (p0) REVERT: G 151 ASP cc_start: 0.8516 (t70) cc_final: 0.8221 (p0) REVERT: H 12 PHE cc_start: 0.8344 (m-80) cc_final: 0.7777 (m-10) REVERT: H 60 ASP cc_start: 0.6996 (m-30) cc_final: 0.6692 (m-30) REVERT: I 89 GLN cc_start: 0.7845 (mp10) cc_final: 0.7197 (mp10) REVERT: J 62 ASP cc_start: 0.8385 (t0) cc_final: 0.8163 (t0) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.2378 time to fit residues: 74.6614 Evaluate side-chains 161 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 42 optimal weight: 50.0000 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 50.0000 chunk 97 optimal weight: 30.0000 chunk 33 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 73 optimal weight: 40.0000 chunk 107 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 141 optimal weight: 40.0000 overall best weight: 11.7996 ------------------------------------------------------------------------------- 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** ** B 36 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** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN ** H 18 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.066300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.060112 restraints weight = 59354.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.061838 restraints weight = 34809.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.062992 restraints weight = 22243.016| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12166 Z= 0.182 Angle : 0.580 5.564 16632 Z= 0.315 Chirality : 0.041 0.136 2079 Planarity : 0.003 0.031 2222 Dihedral : 5.009 22.446 1760 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.19), residues: 1694 helix: None (None), residues: 0 sheet: -0.89 (0.21), residues: 495 loop : -1.73 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 11 PHE 0.016 0.002 PHE G 118 TYR 0.013 0.003 TYR B 158 ARG 0.003 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 296) hydrogen bonds : angle 9.46969 ( 690) SS BOND : bond 0.00495 ( 11) SS BOND : angle 1.49680 ( 22) covalent geometry : bond 0.00383 (12155) covalent geometry : angle 0.57811 (16610) *********************** 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 192 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7153 (m-30) cc_final: 0.6741 (m-30) REVERT: B 60 ASP cc_start: 0.7305 (m-30) cc_final: 0.6916 (m-30) REVERT: B 62 ASP cc_start: 0.8812 (t0) cc_final: 0.8567 (t0) REVERT: C 60 ASP cc_start: 0.7308 (m-30) cc_final: 0.6837 (m-30) REVERT: C 79 ASP cc_start: 0.7398 (m-30) cc_final: 0.6991 (p0) REVERT: D 12 PHE cc_start: 0.8442 (m-10) cc_final: 0.8164 (m-10) REVERT: D 62 ASP cc_start: 0.8662 (t0) cc_final: 0.8397 (t0) REVERT: E 60 ASP cc_start: 0.7322 (m-30) cc_final: 0.7044 (m-30) REVERT: E 151 ASP cc_start: 0.8582 (t0) cc_final: 0.8033 (p0) REVERT: F 60 ASP cc_start: 0.7095 (m-30) cc_final: 0.6767 (m-30) REVERT: F 89 GLN cc_start: 0.8324 (mp10) cc_final: 0.7796 (tp-100) REVERT: F 151 ASP cc_start: 0.8552 (t70) cc_final: 0.7932 (p0) REVERT: G 15 GLU cc_start: 0.8161 (pp20) cc_final: 0.7664 (pp20) REVERT: G 79 ASP cc_start: 0.7431 (m-30) cc_final: 0.7035 (p0) REVERT: G 151 ASP cc_start: 0.8493 (t70) cc_final: 0.8243 (p0) REVERT: H 12 PHE cc_start: 0.8348 (m-80) cc_final: 0.7970 (m-80) REVERT: H 60 ASP cc_start: 0.7112 (m-30) cc_final: 0.6732 (m-30) REVERT: I 33 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8584 (tp40) REVERT: I 84 ASN cc_start: 0.8948 (m-40) cc_final: 0.8326 (p0) REVERT: J 98 ASN cc_start: 0.8443 (m-40) cc_final: 0.8242 (m-40) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2283 time to fit residues: 67.6388 Evaluate side-chains 151 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 30.0000 chunk 57 optimal weight: 30.0000 chunk 34 optimal weight: 50.0000 chunk 145 optimal weight: 50.0000 chunk 5 optimal weight: 30.0000 chunk 133 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 127 optimal weight: 50.0000 chunk 44 optimal weight: 40.0000 chunk 158 optimal weight: 40.0000 chunk 74 optimal weight: 40.0000 overall best weight: 28.0000 ------------------------------------------------------------------------------- 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** B 36 GLN ** 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** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.062311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056248 restraints weight = 60831.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057914 restraints weight = 34969.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059022 restraints weight = 22266.150| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.7185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 12166 Z= 0.377 Angle : 0.779 7.606 16632 Z= 0.432 Chirality : 0.045 0.243 2079 Planarity : 0.004 0.029 2222 Dihedral : 6.533 27.252 1760 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.18), residues: 1694 helix: None (None), residues: 0 sheet: -1.31 (0.21), residues: 495 loop : -2.09 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS A 11 PHE 0.019 0.003 PHE H 118 TYR 0.017 0.003 TYR E 137 ARG 0.007 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 296) hydrogen bonds : angle 10.62923 ( 690) SS BOND : bond 0.00738 ( 11) SS BOND : angle 1.79471 ( 22) covalent geometry : bond 0.00780 (12155) covalent geometry : angle 0.77651 (16610) ********************** 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 157 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7316 (m-30) cc_final: 0.6950 (m-30) REVERT: B 60 ASP cc_start: 0.7463 (m-30) cc_final: 0.7055 (m-30) REVERT: D 12 PHE cc_start: 0.8468 (m-10) cc_final: 0.8167 (m-10) REVERT: D 60 ASP cc_start: 0.7544 (m-30) cc_final: 0.7106 (m-30) REVERT: D 88 LEU cc_start: 0.9014 (mt) cc_final: 0.8788 (mt) REVERT: D 154 PHE cc_start: 0.7663 (t80) cc_final: 0.7339 (t80) REVERT: E 33 GLN cc_start: 0.9125 (tp40) cc_final: 0.8365 (tm-30) REVERT: E 60 ASP cc_start: 0.7537 (m-30) cc_final: 0.7204 (m-30) REVERT: F 60 ASP cc_start: 0.7346 (m-30) cc_final: 0.7076 (m-30) REVERT: F 103 ILE cc_start: 0.9079 (tp) cc_final: 0.8833 (mm) REVERT: F 151 ASP cc_start: 0.8668 (t70) cc_final: 0.8342 (t0) REVERT: H 60 ASP cc_start: 0.7535 (m-30) cc_final: 0.7074 (m-30) REVERT: I 154 PHE cc_start: 0.7913 (t80) cc_final: 0.7554 (t80) REVERT: J 79 ASP cc_start: 0.7512 (m-30) cc_final: 0.6848 (p0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2024 time to fit residues: 49.4368 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 : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 40.0000 chunk 130 optimal weight: 40.0000 chunk 147 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 9 optimal weight: 50.0000 chunk 120 optimal weight: 30.0000 chunk 84 optimal weight: 0.3980 chunk 14 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 overall best weight: 7.2790 ------------------------------------------------------------------------------- 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** ** 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** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN H 18 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 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 = 0.3352 r_free = 0.3352 target = 0.065501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059327 restraints weight = 59558.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.061035 restraints weight = 34749.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.062188 restraints weight = 22292.908| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12166 Z= 0.144 Angle : 0.601 6.566 16632 Z= 0.322 Chirality : 0.043 0.157 2079 Planarity : 0.003 0.038 2222 Dihedral : 5.296 23.695 1760 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.19), residues: 1694 helix: -2.20 (0.68), residues: 66 sheet: -1.13 (0.21), residues: 495 loop : -1.92 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 11 PHE 0.021 0.002 PHE E 118 TYR 0.014 0.003 TYR B 158 ARG 0.002 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 296) hydrogen bonds : angle 9.70244 ( 690) SS BOND : bond 0.00330 ( 11) SS BOND : angle 1.57221 ( 22) covalent geometry : bond 0.00316 (12155) covalent geometry : angle 0.59830 (16610) =============================================================================== Job complete usr+sys time: 3390.05 seconds wall clock time: 63 minutes 21.03 seconds (3801.03 seconds total)