Starting phenix.real_space_refine on Wed Mar 4 21:52:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zxo_15012/03_2026/7zxo_15012.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zxo_15012/03_2026/7zxo_15012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zxo_15012/03_2026/7zxo_15012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zxo_15012/03_2026/7zxo_15012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zxo_15012/03_2026/7zxo_15012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zxo_15012/03_2026/7zxo_15012.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 11328 2.51 5 N 2712 2.21 5 O 2820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17016 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 1.75, per 1000 atoms: 0.10 Number of scatterers: 17016 At special positions: 0 Unit cell: (103.986, 93.522, 153.69, 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 156 16.00 O 2820 8.00 N 2712 7.00 C 11328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 168 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 168 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 168 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 168 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 168 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 168 " 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: 1.51 Conformation dependent library (CDL) restraints added in 747.8 milliseconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 74.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 103 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 157 Processing helix chain 'A' and resid 183 through 217 Processing helix chain 'B' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 103 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 157 Processing helix chain 'B' and resid 183 through 217 Processing helix chain 'C' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 103 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 157 Processing helix chain 'C' and resid 183 through 217 Processing helix chain 'D' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG D 22 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 103 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 157 Processing helix chain 'D' and resid 183 through 217 Processing helix chain 'E' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 103 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 157 Processing helix chain 'E' and resid 183 through 217 Processing helix chain 'F' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG F 22 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 103 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 157 Processing helix chain 'F' and resid 183 through 217 Processing helix chain 'G' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL G 23 " --> pdb=" O ALA G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 103 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 157 Processing helix chain 'G' and resid 183 through 217 Processing helix chain 'H' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL H 23 " --> pdb=" O ALA H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 103 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 157 Processing helix chain 'H' and resid 183 through 217 Processing helix chain 'I' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 103 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 157 Processing helix chain 'I' and resid 183 through 217 Processing helix chain 'J' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG J 22 " --> pdb=" O THR J 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL J 23 " --> pdb=" O ALA J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 103 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 157 Processing helix chain 'J' and resid 183 through 217 Processing helix chain 'K' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG K 22 " --> pdb=" O THR K 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 103 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 157 Processing helix chain 'K' and resid 183 through 217 Processing helix chain 'L' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG L 22 " --> pdb=" O THR L 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 103 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 157 Processing helix chain 'L' and resid 183 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3996 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: 3.11 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5052 1.35 - 1.46: 4516 1.46 - 1.58: 7712 1.58 - 1.70: 0 1.70 - 1.81: 216 Bond restraints: 17496 Sorted by residual: bond pdb=" CB PRO B 87 " pdb=" CG PRO B 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO H 87 " pdb=" CG PRO H 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO E 87 " pdb=" CG PRO E 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO F 87 " pdb=" CG PRO F 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO C 87 " pdb=" CG PRO C 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 ... (remaining 17491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 23320 1.42 - 2.84: 488 2.84 - 4.27: 60 4.27 - 5.69: 24 5.69 - 7.11: 12 Bond angle restraints: 23904 Sorted by residual: angle pdb=" CA PRO D 87 " pdb=" N PRO D 87 " pdb=" CD PRO D 87 " ideal model delta sigma weight residual 112.00 104.89 7.11 1.40e+00 5.10e-01 2.58e+01 angle pdb=" CA PRO K 87 " pdb=" N PRO K 87 " pdb=" CD PRO K 87 " ideal model delta sigma weight residual 112.00 104.90 7.10 1.40e+00 5.10e-01 2.57e+01 angle pdb=" CA PRO E 87 " pdb=" N PRO E 87 " pdb=" CD PRO E 87 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" CA PRO J 87 " pdb=" N PRO J 87 " pdb=" CD PRO J 87 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" CA PRO B 87 " pdb=" N PRO B 87 " pdb=" CD PRO B 87 " ideal model delta sigma weight residual 112.00 104.93 7.07 1.40e+00 5.10e-01 2.55e+01 ... (remaining 23899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 8328 11.94 - 23.87: 1080 23.87 - 35.81: 540 35.81 - 47.74: 120 47.74 - 59.68: 120 Dihedral angle restraints: 10188 sinusoidal: 3888 harmonic: 6300 Sorted by residual: dihedral pdb=" CB CYS J 60 " pdb=" SG CYS J 60 " pdb=" SG CYS J 173 " pdb=" CB CYS J 173 " ideal model delta sinusoidal sigma weight residual 93.00 126.64 -33.64 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CB CYS D 60 " pdb=" SG CYS D 60 " pdb=" SG CYS D 173 " pdb=" CB CYS D 173 " ideal model delta sinusoidal sigma weight residual 93.00 126.62 -33.62 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 173 " pdb=" CB CYS B 173 " ideal model delta sinusoidal sigma weight residual 93.00 126.62 -33.62 1 1.00e+01 1.00e-02 1.61e+01 ... (remaining 10185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2018 0.035 - 0.070: 607 0.070 - 0.105: 187 0.105 - 0.140: 20 0.140 - 0.175: 24 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CA THR E 86 " pdb=" N THR E 86 " pdb=" C THR E 86 " pdb=" CB THR E 86 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA THR D 86 " pdb=" N THR D 86 " pdb=" C THR D 86 " pdb=" CB THR D 86 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA THR L 86 " pdb=" N THR L 86 " pdb=" C THR L 86 " pdb=" CB THR L 86 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 2853 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 86 " -0.080 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO K 87 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO K 87 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO K 87 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 86 " -0.080 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO D 87 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 86 " 0.080 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO G 87 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO G 87 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 87 " 0.064 5.00e-02 4.00e+02 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1982 2.75 - 3.29: 17283 3.29 - 3.83: 31280 3.83 - 4.36: 31344 4.36 - 4.90: 56891 Nonbonded interactions: 138780 Sorted by model distance: nonbonded pdb=" O ARG G 22 " pdb=" OG SER G 26 " model vdw 2.216 3.040 nonbonded pdb=" O ARG A 22 " pdb=" OG SER A 26 " model vdw 2.216 3.040 nonbonded pdb=" O ARG E 22 " pdb=" OG SER E 26 " model vdw 2.217 3.040 nonbonded pdb=" O ARG K 22 " pdb=" OG SER K 26 " model vdw 2.217 3.040 nonbonded pdb=" O ARG J 22 " pdb=" OG SER J 26 " model vdw 2.217 3.040 ... (remaining 138775 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: 0.05 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' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.200 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:7.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.003 0.086 17532 Z= 0.130 Angle : 0.523 7.112 23976 Z= 0.305 Chirality : 0.040 0.175 2856 Planarity : 0.008 0.117 2856 Dihedral : 15.391 59.678 5976 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.36 % Allowed : 19.39 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.19 (0.16), residues: 2076 helix: 4.15 (0.10), residues: 1500 sheet: 1.48 (0.48), residues: 132 loop : -2.28 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 164 TYR 0.008 0.001 TYR J 65 PHE 0.011 0.001 PHE I 180 TRP 0.011 0.001 TRP B 132 HIS 0.002 0.001 HIS K 94 Details of bonding type rmsd covalent geometry : bond 0.00311 (17496) covalent geometry : angle 0.52335 (23904) SS BOND : bond 0.00115 ( 36) SS BOND : angle 0.56978 ( 72) hydrogen bonds : bond 0.08565 ( 1344) hydrogen bonds : angle 3.54432 ( 3996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 298 time to evaluate : 0.663 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 322 average time/residue: 0.5551 time to fit residues: 200.9456 Evaluate side-chains 248 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS E 97 HIS G 97 HIS H 97 HIS I 97 HIS K 97 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.111836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.076581 restraints weight = 24823.942| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.02 r_work: 0.2820 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 17532 Z= 0.126 Angle : 0.474 4.958 23976 Z= 0.258 Chirality : 0.040 0.159 2856 Planarity : 0.006 0.080 2856 Dihedral : 3.884 14.873 2292 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.35 % Allowed : 19.86 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.22 (0.16), residues: 2076 helix: 4.18 (0.10), residues: 1488 sheet: 1.71 (0.49), residues: 132 loop : -2.18 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 75 TYR 0.010 0.001 TYR J 65 PHE 0.012 0.001 PHE H 180 TRP 0.007 0.001 TRP J 132 HIS 0.003 0.001 HIS K 97 Details of bonding type rmsd covalent geometry : bond 0.00274 (17496) covalent geometry : angle 0.47418 (23904) SS BOND : bond 0.00067 ( 36) SS BOND : angle 0.55749 ( 72) hydrogen bonds : bond 0.03923 ( 1344) hydrogen bonds : angle 3.31919 ( 3996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 250 time to evaluate : 0.654 Fit side-chains REVERT: A 93 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.7799 (mpp) REVERT: D 93 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.7808 (mpp) REVERT: G 93 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.7799 (mpp) REVERT: J 93 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.7805 (mpp) outliers start: 64 outliers final: 17 residues processed: 290 average time/residue: 0.5573 time to fit residues: 181.7997 Evaluate side-chains 257 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 69 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** 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 = 0.3597 r_free = 0.3597 target = 0.112025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.076875 restraints weight = 24931.176| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.03 r_work: 0.2823 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17532 Z= 0.104 Angle : 0.439 5.150 23976 Z= 0.237 Chirality : 0.038 0.154 2856 Planarity : 0.005 0.066 2856 Dihedral : 3.755 15.232 2280 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.51 % Allowed : 18.71 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.32 (0.16), residues: 2076 helix: 4.27 (0.09), residues: 1488 sheet: 1.83 (0.50), residues: 132 loop : -2.26 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 75 TYR 0.008 0.001 TYR J 65 PHE 0.010 0.001 PHE H 180 TRP 0.006 0.001 TRP J 132 HIS 0.003 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00224 (17496) covalent geometry : angle 0.43837 (23904) SS BOND : bond 0.00046 ( 36) SS BOND : angle 0.49635 ( 72) hydrogen bonds : bond 0.03650 ( 1344) hydrogen bonds : angle 3.21027 ( 3996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 0.711 Fit side-chains REVERT: A 22 ARG cc_start: 0.5159 (OUTLIER) cc_final: 0.4129 (tpp-160) REVERT: A 34 MET cc_start: 0.8814 (mmm) cc_final: 0.8336 (mtm) REVERT: A 93 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.7893 (mpp) REVERT: B 22 ARG cc_start: 0.5139 (OUTLIER) cc_final: 0.4063 (tpp-160) REVERT: B 93 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8035 (mpp) REVERT: B 97 HIS cc_start: 0.8128 (t-170) cc_final: 0.7684 (t-170) REVERT: C 22 ARG cc_start: 0.5145 (OUTLIER) cc_final: 0.3849 (ttt180) REVERT: C 97 HIS cc_start: 0.8173 (t-170) cc_final: 0.7750 (t-170) REVERT: D 22 ARG cc_start: 0.5167 (OUTLIER) cc_final: 0.4135 (tpp-160) REVERT: D 93 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.7894 (mpp) REVERT: E 22 ARG cc_start: 0.5115 (OUTLIER) cc_final: 0.4066 (tpp-160) REVERT: E 93 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8012 (mpp) REVERT: E 97 HIS cc_start: 0.8144 (t-170) cc_final: 0.7704 (t-170) REVERT: F 22 ARG cc_start: 0.5165 (OUTLIER) cc_final: 0.3854 (ttt180) REVERT: F 97 HIS cc_start: 0.8171 (t-170) cc_final: 0.7737 (t-170) REVERT: G 22 ARG cc_start: 0.5169 (OUTLIER) cc_final: 0.4141 (tpp-160) REVERT: G 34 MET cc_start: 0.8806 (mmm) cc_final: 0.8334 (mtm) REVERT: G 93 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.7891 (mpp) REVERT: H 22 ARG cc_start: 0.5146 (OUTLIER) cc_final: 0.4068 (tpp-160) REVERT: H 93 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8007 (mpp) REVERT: H 97 HIS cc_start: 0.8131 (t-170) cc_final: 0.7683 (t-170) REVERT: I 22 ARG cc_start: 0.5159 (OUTLIER) cc_final: 0.3841 (ttt180) REVERT: I 97 HIS cc_start: 0.8192 (t-170) cc_final: 0.7760 (t-170) REVERT: J 22 ARG cc_start: 0.5155 (OUTLIER) cc_final: 0.4113 (tpp-160) REVERT: J 34 MET cc_start: 0.8816 (mmm) cc_final: 0.8337 (mtm) REVERT: J 93 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.7889 (mpp) REVERT: K 22 ARG cc_start: 0.5136 (OUTLIER) cc_final: 0.4097 (tpp-160) REVERT: K 93 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8027 (mpp) REVERT: K 97 HIS cc_start: 0.8135 (t-170) cc_final: 0.7707 (t-170) REVERT: L 22 ARG cc_start: 0.5166 (OUTLIER) cc_final: 0.3859 (ttt180) REVERT: L 97 HIS cc_start: 0.8136 (t-170) cc_final: 0.7713 (t-170) outliers start: 67 outliers final: 22 residues processed: 283 average time/residue: 0.6572 time to fit residues: 204.7227 Evaluate side-chains 266 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 22 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 22 ARG Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 22 ARG Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 203 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.071994 restraints weight = 24817.094| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.99 r_work: 0.2735 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17532 Z= 0.181 Angle : 0.501 5.196 23976 Z= 0.270 Chirality : 0.041 0.175 2856 Planarity : 0.004 0.054 2856 Dihedral : 3.854 14.711 2280 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.04 % Allowed : 18.66 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.05 (0.16), residues: 2076 helix: 4.04 (0.10), residues: 1488 sheet: 1.52 (0.47), residues: 132 loop : -2.15 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 164 TYR 0.016 0.002 TYR J 65 PHE 0.013 0.002 PHE A 180 TRP 0.006 0.001 TRP J 132 HIS 0.003 0.001 HIS L 97 Details of bonding type rmsd covalent geometry : bond 0.00434 (17496) covalent geometry : angle 0.50041 (23904) SS BOND : bond 0.00109 ( 36) SS BOND : angle 0.62195 ( 72) hydrogen bonds : bond 0.04403 ( 1344) hydrogen bonds : angle 3.34516 ( 3996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 206 time to evaluate : 0.447 Fit side-chains REVERT: A 34 MET cc_start: 0.8874 (mmm) cc_final: 0.8412 (mtm) REVERT: A 93 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.7934 (mpp) REVERT: D 34 MET cc_start: 0.8869 (mmm) cc_final: 0.8414 (mtm) REVERT: D 93 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.7940 (mpp) REVERT: G 34 MET cc_start: 0.8865 (mmm) cc_final: 0.8407 (mtm) REVERT: G 93 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.7937 (mpp) REVERT: J 34 MET cc_start: 0.8890 (mmm) cc_final: 0.8421 (mtm) REVERT: J 93 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.7938 (mpp) outliers start: 58 outliers final: 31 residues processed: 253 average time/residue: 0.5081 time to fit residues: 144.9414 Evaluate side-chains 241 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 52 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 166 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** 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 = 0.3516 r_free = 0.3516 target = 0.106289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.071392 restraints weight = 24614.667| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.95 r_work: 0.2717 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17532 Z= 0.205 Angle : 0.522 5.221 23976 Z= 0.282 Chirality : 0.042 0.170 2856 Planarity : 0.004 0.048 2856 Dihedral : 3.910 15.856 2280 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.77 % Allowed : 19.39 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.76 (0.16), residues: 2076 helix: 3.79 (0.10), residues: 1488 sheet: 1.40 (0.47), residues: 132 loop : -2.07 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 22 TYR 0.016 0.002 TYR B 65 PHE 0.016 0.002 PHE E 180 TRP 0.007 0.001 TRP G 133 HIS 0.003 0.001 HIS K 97 Details of bonding type rmsd covalent geometry : bond 0.00500 (17496) covalent geometry : angle 0.52152 (23904) SS BOND : bond 0.00127 ( 36) SS BOND : angle 0.76646 ( 72) hydrogen bonds : bond 0.04638 ( 1344) hydrogen bonds : angle 3.39320 ( 3996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 216 time to evaluate : 0.678 Fit side-chains REVERT: A 34 MET cc_start: 0.8868 (mmm) cc_final: 0.8407 (mtm) REVERT: A 93 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.7963 (mpp) REVERT: A 211 TYR cc_start: 0.8568 (t80) cc_final: 0.8309 (t80) REVERT: C 156 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8920 (mp) REVERT: C 211 TYR cc_start: 0.8558 (t80) cc_final: 0.8357 (t80) REVERT: D 34 MET cc_start: 0.8850 (mmm) cc_final: 0.8394 (mtm) REVERT: D 93 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.7973 (mpp) REVERT: D 211 TYR cc_start: 0.8570 (t80) cc_final: 0.8306 (t80) REVERT: F 156 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8914 (mp) REVERT: F 211 TYR cc_start: 0.8570 (t80) cc_final: 0.8368 (t80) REVERT: G 34 MET cc_start: 0.8875 (mmm) cc_final: 0.8407 (mtm) REVERT: G 93 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.7937 (mpp) REVERT: G 211 TYR cc_start: 0.8566 (t80) cc_final: 0.8308 (t80) REVERT: I 156 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8917 (mp) REVERT: I 211 TYR cc_start: 0.8577 (t80) cc_final: 0.8366 (t80) REVERT: J 34 MET cc_start: 0.8879 (mmm) cc_final: 0.8410 (mtm) REVERT: J 93 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.7975 (mpp) REVERT: J 211 TYR cc_start: 0.8562 (t80) cc_final: 0.8294 (t80) REVERT: L 156 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8918 (mp) REVERT: L 211 TYR cc_start: 0.8543 (t80) cc_final: 0.8342 (t80) outliers start: 72 outliers final: 41 residues processed: 274 average time/residue: 0.5669 time to fit residues: 173.7707 Evaluate side-chains 265 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 156 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 202 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 122 optimal weight: 0.1980 chunk 162 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 98 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 98 GLN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS G 98 GLN ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS J 98 GLN ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.075248 restraints weight = 24685.042| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.93 r_work: 0.2790 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17532 Z= 0.104 Angle : 0.449 4.805 23976 Z= 0.241 Chirality : 0.038 0.153 2856 Planarity : 0.003 0.043 2856 Dihedral : 3.732 15.281 2280 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.67 % Allowed : 21.23 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.16 (0.17), residues: 2076 helix: 4.15 (0.10), residues: 1488 sheet: 1.55 (0.49), residues: 132 loop : -2.23 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 22 TYR 0.007 0.001 TYR J 65 PHE 0.009 0.001 PHE K 180 TRP 0.007 0.001 TRP L 132 HIS 0.002 0.001 HIS K 97 Details of bonding type rmsd covalent geometry : bond 0.00227 (17496) covalent geometry : angle 0.44892 (23904) SS BOND : bond 0.00051 ( 36) SS BOND : angle 0.49056 ( 72) hydrogen bonds : bond 0.03707 ( 1344) hydrogen bonds : angle 3.19926 ( 3996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.573 Fit side-chains REVERT: A 34 MET cc_start: 0.8821 (mmm) cc_final: 0.8310 (mtm) REVERT: A 211 TYR cc_start: 0.8564 (t80) cc_final: 0.8335 (t80) REVERT: D 34 MET cc_start: 0.8791 (mmm) cc_final: 0.8321 (mtm) REVERT: D 211 TYR cc_start: 0.8574 (t80) cc_final: 0.8345 (t80) REVERT: F 211 TYR cc_start: 0.8569 (t80) cc_final: 0.8355 (t80) REVERT: G 34 MET cc_start: 0.8819 (mmm) cc_final: 0.8303 (mtm) REVERT: G 211 TYR cc_start: 0.8572 (t80) cc_final: 0.8345 (t80) REVERT: I 211 TYR cc_start: 0.8581 (t80) cc_final: 0.8344 (t80) REVERT: J 34 MET cc_start: 0.8821 (mmm) cc_final: 0.8312 (mtm) REVERT: J 211 TYR cc_start: 0.8571 (t80) cc_final: 0.8342 (t80) REVERT: L 211 TYR cc_start: 0.8572 (t80) cc_final: 0.8360 (t80) outliers start: 51 outliers final: 13 residues processed: 278 average time/residue: 0.5862 time to fit residues: 181.4479 Evaluate side-chains 233 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 220 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 31 optimal weight: 0.0020 chunk 161 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 191 optimal weight: 0.4980 chunk 97 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.074527 restraints weight = 24680.041| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.98 r_work: 0.2791 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17532 Z= 0.105 Angle : 0.454 4.898 23976 Z= 0.243 Chirality : 0.038 0.155 2856 Planarity : 0.003 0.041 2856 Dihedral : 3.614 14.618 2280 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.52 % Allowed : 22.48 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.25 (0.16), residues: 2076 helix: 4.23 (0.10), residues: 1488 sheet: 1.73 (0.50), residues: 132 loop : -2.27 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 32 TYR 0.009 0.001 TYR K 65 PHE 0.009 0.001 PHE B 180 TRP 0.006 0.001 TRP F 132 HIS 0.004 0.001 HIS K 97 Details of bonding type rmsd covalent geometry : bond 0.00234 (17496) covalent geometry : angle 0.45408 (23904) SS BOND : bond 0.00051 ( 36) SS BOND : angle 0.48944 ( 72) hydrogen bonds : bond 0.03580 ( 1344) hydrogen bonds : angle 3.12193 ( 3996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.653 Fit side-chains REVERT: A 34 MET cc_start: 0.8848 (mmm) cc_final: 0.8345 (mtm) REVERT: A 215 ARG cc_start: 0.7884 (mpt180) cc_final: 0.7644 (mmt90) REVERT: B 215 ARG cc_start: 0.7933 (mpt180) cc_final: 0.7606 (mmt90) REVERT: C 215 ARG cc_start: 0.7964 (mpt180) cc_final: 0.7759 (mmt90) REVERT: D 34 MET cc_start: 0.8811 (mmm) cc_final: 0.8329 (mtm) REVERT: D 215 ARG cc_start: 0.7874 (mpt180) cc_final: 0.7645 (mmt90) REVERT: E 215 ARG cc_start: 0.7932 (mpt180) cc_final: 0.7610 (mmt90) REVERT: F 211 TYR cc_start: 0.8571 (t80) cc_final: 0.8366 (t80) REVERT: F 215 ARG cc_start: 0.7948 (mpt180) cc_final: 0.7738 (mmt90) REVERT: G 34 MET cc_start: 0.8839 (mmm) cc_final: 0.8342 (mtm) REVERT: G 215 ARG cc_start: 0.7872 (mpt180) cc_final: 0.7644 (mmt90) REVERT: H 215 ARG cc_start: 0.7938 (mpt180) cc_final: 0.7602 (mmt90) REVERT: I 211 TYR cc_start: 0.8580 (t80) cc_final: 0.8351 (t80) REVERT: J 34 MET cc_start: 0.8838 (mmm) cc_final: 0.8336 (mtm) REVERT: J 215 ARG cc_start: 0.7867 (mpt180) cc_final: 0.7625 (mmt90) REVERT: K 215 ARG cc_start: 0.7926 (mpt180) cc_final: 0.7603 (mmt90) REVERT: L 211 TYR cc_start: 0.8566 (t80) cc_final: 0.8363 (t80) REVERT: L 215 ARG cc_start: 0.7951 (mpt180) cc_final: 0.7740 (mmt90) outliers start: 29 outliers final: 17 residues processed: 262 average time/residue: 0.6505 time to fit residues: 188.0460 Evaluate side-chains 247 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 176 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 160 optimal weight: 5.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.075250 restraints weight = 24821.379| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.00 r_work: 0.2805 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17532 Z= 0.104 Angle : 0.457 4.808 23976 Z= 0.245 Chirality : 0.038 0.153 2856 Planarity : 0.003 0.040 2856 Dihedral : 3.535 14.609 2280 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.94 % Allowed : 22.69 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.32 (0.16), residues: 2076 helix: 4.26 (0.10), residues: 1488 sheet: 1.86 (0.51), residues: 132 loop : -2.19 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 32 TYR 0.008 0.001 TYR E 65 PHE 0.009 0.001 PHE E 180 TRP 0.006 0.001 TRP I 132 HIS 0.006 0.001 HIS L 97 Details of bonding type rmsd covalent geometry : bond 0.00231 (17496) covalent geometry : angle 0.45690 (23904) SS BOND : bond 0.00060 ( 36) SS BOND : angle 0.47329 ( 72) hydrogen bonds : bond 0.03452 ( 1344) hydrogen bonds : angle 3.07657 ( 3996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.602 Fit side-chains REVERT: A 34 MET cc_start: 0.8844 (mmm) cc_final: 0.8364 (mtm) REVERT: A 211 TYR cc_start: 0.8451 (t80) cc_final: 0.8177 (t80) REVERT: B 97 HIS cc_start: 0.7903 (t-90) cc_final: 0.7647 (t-90) REVERT: C 97 HIS cc_start: 0.7881 (t-90) cc_final: 0.7626 (t-90) REVERT: D 34 MET cc_start: 0.8804 (mmm) cc_final: 0.8344 (mtm) REVERT: E 97 HIS cc_start: 0.7906 (t-90) cc_final: 0.7659 (t-90) REVERT: F 97 HIS cc_start: 0.7913 (t-90) cc_final: 0.7637 (t-170) REVERT: F 211 TYR cc_start: 0.8555 (t80) cc_final: 0.8316 (t80) REVERT: G 34 MET cc_start: 0.8831 (mmm) cc_final: 0.8359 (mtm) REVERT: H 97 HIS cc_start: 0.7980 (t-90) cc_final: 0.7716 (t-90) REVERT: I 97 HIS cc_start: 0.7877 (t-90) cc_final: 0.7618 (t-90) REVERT: J 34 MET cc_start: 0.8829 (mmm) cc_final: 0.8354 (mtm) REVERT: J 211 TYR cc_start: 0.8447 (t80) cc_final: 0.8171 (t80) REVERT: K 97 HIS cc_start: 0.7922 (t-90) cc_final: 0.7671 (t-90) REVERT: L 97 HIS cc_start: 0.7903 (t-90) cc_final: 0.7635 (t-170) REVERT: L 211 TYR cc_start: 0.8557 (t80) cc_final: 0.8320 (t80) outliers start: 37 outliers final: 14 residues processed: 265 average time/residue: 0.6229 time to fit residues: 182.9011 Evaluate side-chains 242 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 162 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.107839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.073071 restraints weight = 24779.379| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.99 r_work: 0.2761 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17532 Z= 0.131 Angle : 0.483 4.947 23976 Z= 0.259 Chirality : 0.039 0.157 2856 Planarity : 0.004 0.040 2856 Dihedral : 3.597 14.631 2280 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.26 % Allowed : 23.58 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.18 (0.16), residues: 2076 helix: 4.13 (0.10), residues: 1488 sheet: 1.83 (0.50), residues: 132 loop : -2.18 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 215 TYR 0.013 0.001 TYR E 65 PHE 0.012 0.002 PHE A 180 TRP 0.005 0.001 TRP A 132 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00311 (17496) covalent geometry : angle 0.48252 (23904) SS BOND : bond 0.00041 ( 36) SS BOND : angle 0.54107 ( 72) hydrogen bonds : bond 0.03791 ( 1344) hydrogen bonds : angle 3.12869 ( 3996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.719 Fit side-chains REVERT: A 34 MET cc_start: 0.8851 (mmm) cc_final: 0.8359 (mtm) REVERT: A 156 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8836 (mp) REVERT: A 211 TYR cc_start: 0.8448 (t80) cc_final: 0.8169 (t80) REVERT: A 215 ARG cc_start: 0.7864 (mpt180) cc_final: 0.7518 (mmt90) REVERT: B 97 HIS cc_start: 0.7983 (t-90) cc_final: 0.7728 (t-90) REVERT: B 215 ARG cc_start: 0.7876 (mpt180) cc_final: 0.7670 (mmt90) REVERT: C 97 HIS cc_start: 0.7934 (t-90) cc_final: 0.7683 (t-90) REVERT: D 34 MET cc_start: 0.8825 (mmm) cc_final: 0.8346 (mtm) REVERT: D 215 ARG cc_start: 0.7850 (mpt180) cc_final: 0.7541 (mmt90) REVERT: E 97 HIS cc_start: 0.7978 (t-90) cc_final: 0.7724 (t-90) REVERT: E 215 ARG cc_start: 0.7841 (mmt90) cc_final: 0.7635 (mpt180) REVERT: F 97 HIS cc_start: 0.7937 (t-90) cc_final: 0.7687 (t-170) REVERT: F 211 TYR cc_start: 0.8525 (t80) cc_final: 0.8316 (t80) REVERT: G 34 MET cc_start: 0.8838 (mmm) cc_final: 0.8349 (mtm) REVERT: G 156 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8841 (mp) REVERT: G 215 ARG cc_start: 0.7855 (mpt180) cc_final: 0.7546 (mmt90) REVERT: H 97 HIS cc_start: 0.7968 (t-90) cc_final: 0.7729 (t-90) REVERT: H 215 ARG cc_start: 0.7856 (mpt180) cc_final: 0.7521 (mmt90) REVERT: I 97 HIS cc_start: 0.7916 (t-90) cc_final: 0.7657 (t-90) REVERT: J 34 MET cc_start: 0.8837 (mmm) cc_final: 0.8352 (mtm) REVERT: J 156 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8869 (mp) REVERT: J 211 TYR cc_start: 0.8445 (t80) cc_final: 0.8224 (t80) REVERT: J 215 ARG cc_start: 0.7859 (mpt180) cc_final: 0.7510 (mmt90) REVERT: K 97 HIS cc_start: 0.7961 (t-90) cc_final: 0.7718 (t-90) REVERT: K 215 ARG cc_start: 0.7849 (mmt90) cc_final: 0.7643 (mpt180) REVERT: L 97 HIS cc_start: 0.7912 (t-90) cc_final: 0.7669 (t-90) REVERT: L 211 TYR cc_start: 0.8523 (t80) cc_final: 0.8312 (t80) outliers start: 24 outliers final: 14 residues processed: 251 average time/residue: 0.6324 time to fit residues: 175.7173 Evaluate side-chains 245 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 0.0270 chunk 127 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 overall best weight: 1.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** 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 = 0.3527 r_free = 0.3527 target = 0.106925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.072366 restraints weight = 24673.114| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.97 r_work: 0.2749 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17532 Z= 0.140 Angle : 0.498 5.624 23976 Z= 0.268 Chirality : 0.040 0.155 2856 Planarity : 0.004 0.040 2856 Dihedral : 3.646 14.749 2280 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.47 % Allowed : 23.79 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.08 (0.16), residues: 2076 helix: 4.05 (0.10), residues: 1488 sheet: 1.69 (0.49), residues: 132 loop : -2.16 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 215 TYR 0.013 0.002 TYR K 171 PHE 0.012 0.002 PHE D 180 TRP 0.005 0.001 TRP J 132 HIS 0.006 0.001 HIS G 97 Details of bonding type rmsd covalent geometry : bond 0.00333 (17496) covalent geometry : angle 0.49778 (23904) SS BOND : bond 0.00074 ( 36) SS BOND : angle 0.54789 ( 72) hydrogen bonds : bond 0.03964 ( 1344) hydrogen bonds : angle 3.16358 ( 3996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.412 Fit side-chains REVERT: A 34 MET cc_start: 0.8855 (mmm) cc_final: 0.8404 (mtm) REVERT: A 211 TYR cc_start: 0.8471 (t80) cc_final: 0.8144 (t80) REVERT: A 215 ARG cc_start: 0.7866 (mpt180) cc_final: 0.7505 (mmt90) REVERT: B 97 HIS cc_start: 0.8002 (t-90) cc_final: 0.7788 (t-90) REVERT: C 97 HIS cc_start: 0.7993 (t-90) cc_final: 0.7793 (t-90) REVERT: C 215 ARG cc_start: 0.7975 (mpt180) cc_final: 0.7678 (mmt90) REVERT: D 34 MET cc_start: 0.8841 (mmm) cc_final: 0.8378 (mtm) REVERT: D 211 TYR cc_start: 0.8457 (t80) cc_final: 0.8184 (t80) REVERT: D 215 ARG cc_start: 0.7840 (mpt180) cc_final: 0.7500 (mmt90) REVERT: E 97 HIS cc_start: 0.8003 (t-90) cc_final: 0.7789 (t-90) REVERT: F 97 HIS cc_start: 0.7952 (t-90) cc_final: 0.7743 (t-90) REVERT: F 215 ARG cc_start: 0.7927 (mpt180) cc_final: 0.7635 (mmt90) REVERT: G 34 MET cc_start: 0.8841 (mmm) cc_final: 0.8397 (mtm) REVERT: G 156 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8864 (mp) REVERT: G 211 TYR cc_start: 0.8462 (t80) cc_final: 0.8194 (t80) REVERT: G 215 ARG cc_start: 0.7856 (mpt180) cc_final: 0.7515 (mmt90) REVERT: H 215 ARG cc_start: 0.7844 (mpt180) cc_final: 0.7554 (mmt90) REVERT: I 97 HIS cc_start: 0.7993 (t-90) cc_final: 0.7787 (t-90) REVERT: I 215 ARG cc_start: 0.7961 (mpt180) cc_final: 0.7719 (mmt90) REVERT: J 34 MET cc_start: 0.8847 (mmm) cc_final: 0.8398 (mtm) REVERT: J 156 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8864 (mp) REVERT: K 97 HIS cc_start: 0.7985 (t-90) cc_final: 0.7779 (t-90) REVERT: L 97 HIS cc_start: 0.7941 (t-90) cc_final: 0.7733 (t-90) REVERT: L 215 ARG cc_start: 0.7925 (mpt180) cc_final: 0.7633 (mmt90) outliers start: 28 outliers final: 14 residues processed: 256 average time/residue: 0.6328 time to fit residues: 179.1260 Evaluate side-chains 244 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 90 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 3 optimal weight: 0.0170 chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 HIS ** 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 = 0.3562 r_free = 0.3562 target = 0.108650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.075079 restraints weight = 25860.878| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.97 r_work: 0.2809 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17532 Z= 0.121 Angle : 0.482 5.107 23976 Z= 0.259 Chirality : 0.039 0.154 2856 Planarity : 0.003 0.039 2856 Dihedral : 3.595 14.724 2280 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.84 % Allowed : 24.42 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.15 (0.16), residues: 2076 helix: 4.11 (0.10), residues: 1488 sheet: 1.74 (0.50), residues: 132 loop : -2.15 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 22 TYR 0.010 0.001 TYR J 65 PHE 0.011 0.001 PHE K 180 TRP 0.005 0.001 TRP D 132 HIS 0.004 0.001 HIS H 97 Details of bonding type rmsd covalent geometry : bond 0.00284 (17496) covalent geometry : angle 0.48199 (23904) SS BOND : bond 0.00041 ( 36) SS BOND : angle 0.52030 ( 72) hydrogen bonds : bond 0.03726 ( 1344) hydrogen bonds : angle 3.12291 ( 3996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6322.48 seconds wall clock time: 108 minutes 19.87 seconds (6499.87 seconds total)