Starting phenix.real_space_refine on Sat Jun 14 23:49:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zxo_15012/06_2025/7zxo_15012.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zxo_15012/06_2025/7zxo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zxo_15012/06_2025/7zxo_15012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zxo_15012/06_2025/7zxo_15012.map" model { file = "/net/cci-nas-00/data/ceres_data/7zxo_15012/06_2025/7zxo_15012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zxo_15012/06_2025/7zxo_15012.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 5.68, per 1000 atoms: 0.33 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 C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 168 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 168 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 168 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 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: 4.36 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.34 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: 5.09 Time building geometry restraints manager: 5.02 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 33.760 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (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 TRP 0.011 0.001 TRP B 132 HIS 0.002 0.001 HIS K 94 PHE 0.011 0.001 PHE I 180 TYR 0.008 0.001 TYR J 65 ARG 0.001 0.000 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.08565 ( 1344) hydrogen bonds : angle 3.54432 ( 3996) SS BOND : bond 0.00115 ( 36) SS BOND : angle 0.56978 ( 72) covalent geometry : bond 0.00311 (17496) covalent geometry : angle 0.52335 (23904) *********************** 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 : 1.734 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 322 average time/residue: 1.0906 time to fit residues: 396.3231 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 : 1.717 ------------------------------------------------------------------------------- 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 172 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 G 97 HIS H 97 HIS I 97 HIS L 97 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.077783 restraints weight = 24829.084| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.03 r_work: 0.2844 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 17532 Z= 0.111 Angle : 0.463 4.934 23976 Z= 0.251 Chirality : 0.039 0.162 2856 Planarity : 0.006 0.081 2856 Dihedral : 3.824 14.950 2292 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.35 % Allowed : 20.28 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.16), residues: 2076 helix: 4.24 (0.09), residues: 1488 sheet: 1.79 (0.49), residues: 132 loop : -2.23 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 132 HIS 0.004 0.001 HIS K 97 PHE 0.010 0.001 PHE H 180 TYR 0.008 0.001 TYR D 65 ARG 0.001 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 1344) hydrogen bonds : angle 3.30972 ( 3996) SS BOND : bond 0.00064 ( 36) SS BOND : angle 0.50061 ( 72) covalent geometry : bond 0.00233 (17496) covalent geometry : angle 0.46320 (23904) *********************** 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 320 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 256 time to evaluate : 1.780 Fit side-chains REVERT: A 22 ARG cc_start: 0.5158 (OUTLIER) cc_final: 0.4049 (tpp-160) REVERT: A 93 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.7792 (mpp) REVERT: B 97 HIS cc_start: 0.8121 (t70) cc_final: 0.7807 (t-170) REVERT: C 22 ARG cc_start: 0.5149 (OUTLIER) cc_final: 0.4055 (ttt180) REVERT: D 22 ARG cc_start: 0.5124 (OUTLIER) cc_final: 0.4040 (tpp-160) REVERT: D 93 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.7812 (mpp) REVERT: D 97 HIS cc_start: 0.8218 (t-170) cc_final: 0.7770 (t-170) REVERT: E 97 HIS cc_start: 0.8226 (t-170) cc_final: 0.7759 (t-170) REVERT: F 22 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.3892 (ttt180) REVERT: G 22 ARG cc_start: 0.5153 (OUTLIER) cc_final: 0.4051 (tpp-160) REVERT: G 93 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.7798 (mpp) REVERT: H 97 HIS cc_start: 0.8127 (t70) cc_final: 0.7804 (t-170) REVERT: I 22 ARG cc_start: 0.5147 (OUTLIER) cc_final: 0.4059 (ttt180) REVERT: J 22 ARG cc_start: 0.5122 (OUTLIER) cc_final: 0.4036 (tpp-160) REVERT: J 93 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.7795 (mpp) REVERT: J 97 HIS cc_start: 0.8210 (t-170) cc_final: 0.7761 (t-170) REVERT: K 97 HIS cc_start: 0.8222 (t-170) cc_final: 0.7763 (t-170) REVERT: L 22 ARG cc_start: 0.5188 (OUTLIER) cc_final: 0.3903 (ttt180) outliers start: 64 outliers final: 16 residues processed: 296 average time/residue: 1.3417 time to fit residues: 438.5137 Evaluate side-chains 264 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 212 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 23 VAL 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 D residue 212 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 23 VAL 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 G residue 212 LEU Chi-restraints excluded: chain H residue 23 VAL 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 J residue 212 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 22 ARG 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 135 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 HIS F 97 HIS I 97 HIS L 97 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.074013 restraints weight = 24831.331| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.97 r_work: 0.2765 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17532 Z= 0.142 Angle : 0.483 5.492 23976 Z= 0.261 Chirality : 0.040 0.173 2856 Planarity : 0.005 0.065 2856 Dihedral : 3.831 15.402 2280 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 4.51 % Allowed : 17.77 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.16), residues: 2076 helix: 4.10 (0.09), residues: 1488 sheet: 1.67 (0.49), residues: 132 loop : -2.06 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.003 0.001 HIS K 97 PHE 0.014 0.002 PHE B 180 TYR 0.013 0.002 TYR D 65 ARG 0.003 0.000 ARG E 22 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 1344) hydrogen bonds : angle 3.25063 ( 3996) SS BOND : bond 0.00080 ( 36) SS BOND : angle 0.57608 ( 72) covalent geometry : bond 0.00334 (17496) covalent geometry : angle 0.48249 (23904) *********************** 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 303 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 217 time to evaluate : 1.820 Fit side-chains REVERT: A 34 MET cc_start: 0.8878 (mmm) cc_final: 0.8408 (mtm) REVERT: A 93 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.7877 (mpp) REVERT: B 22 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.3899 (tpp-160) REVERT: C 97 HIS cc_start: 0.8135 (t70) cc_final: 0.7826 (t-170) REVERT: D 93 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.7930 (mpp) REVERT: E 22 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.3916 (tpp-160) REVERT: F 97 HIS cc_start: 0.8134 (t70) cc_final: 0.7822 (t-170) REVERT: G 34 MET cc_start: 0.8865 (mmm) cc_final: 0.8399 (mtm) REVERT: G 93 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.7895 (mpp) REVERT: H 22 ARG cc_start: 0.5894 (OUTLIER) cc_final: 0.3899 (tpp-160) REVERT: I 97 HIS cc_start: 0.8136 (t70) cc_final: 0.7825 (t-170) REVERT: J 34 MET cc_start: 0.8863 (mmm) cc_final: 0.8400 (mtm) REVERT: J 93 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.7906 (mpp) REVERT: K 22 ARG cc_start: 0.5892 (OUTLIER) cc_final: 0.3904 (tpp-160) REVERT: L 97 HIS cc_start: 0.8144 (t70) cc_final: 0.7831 (t-170) outliers start: 86 outliers final: 29 residues processed: 286 average time/residue: 1.1100 time to fit residues: 360.3095 Evaluate side-chains 244 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 2.013 ------------------------------------------------------------------------------- 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 93 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain D residue 18 THR 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 F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 18 THR 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 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 25 LEU Chi-restraints excluded: chain L residue 18 THR 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 189 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 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 = 0.3554 r_free = 0.3554 target = 0.108848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.073963 restraints weight = 24617.372| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.97 r_work: 0.2772 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17532 Z= 0.129 Angle : 0.459 5.116 23976 Z= 0.248 Chirality : 0.039 0.163 2856 Planarity : 0.004 0.051 2856 Dihedral : 3.756 14.506 2280 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.73 % Allowed : 19.65 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.24 (0.16), residues: 2076 helix: 4.18 (0.09), residues: 1488 sheet: 1.62 (0.48), residues: 132 loop : -2.06 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 132 HIS 0.003 0.001 HIS K 97 PHE 0.011 0.002 PHE K 180 TYR 0.011 0.001 TYR A 65 ARG 0.001 0.000 ARG G 75 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 1344) hydrogen bonds : angle 3.20826 ( 3996) SS BOND : bond 0.00079 ( 36) SS BOND : angle 0.50011 ( 72) covalent geometry : bond 0.00300 (17496) covalent geometry : angle 0.45912 (23904) *********************** 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 266 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 1.812 Fit side-chains REVERT: A 34 MET cc_start: 0.8835 (mmm) cc_final: 0.8396 (mtm) REVERT: A 93 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.7899 (mpp) REVERT: B 93 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.7993 (mpp) REVERT: D 93 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.7908 (mpp) REVERT: E 93 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8015 (mpp) REVERT: G 34 MET cc_start: 0.8823 (mmm) cc_final: 0.8388 (mtm) REVERT: G 93 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.7907 (mpp) REVERT: H 93 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8002 (mpp) REVERT: J 34 MET cc_start: 0.8828 (mmm) cc_final: 0.8393 (mtm) REVERT: J 93 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.7907 (mpp) REVERT: K 93 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8021 (mpp) REVERT: K 97 HIS cc_start: 0.8195 (t-90) cc_final: 0.7991 (t-170) outliers start: 52 outliers final: 31 residues processed: 246 average time/residue: 1.1689 time to fit residues: 323.6415 Evaluate side-chains 253 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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 93 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 VAL 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 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 E residue 93 MET Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 18 THR 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 25 LEU 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 K residue 93 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 178 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS G 97 HIS ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 HIS ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.075874 restraints weight = 24727.310| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.01 r_work: 0.2804 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2011 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 : 0.439 4.885 23976 Z= 0.236 Chirality : 0.038 0.158 2856 Planarity : 0.004 0.045 2856 Dihedral : 3.630 14.534 2280 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.88 % Allowed : 21.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.41 (0.16), residues: 2076 helix: 4.32 (0.09), residues: 1488 sheet: 1.74 (0.49), residues: 132 loop : -2.09 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 132 HIS 0.003 0.001 HIS I 97 PHE 0.009 0.001 PHE E 180 TYR 0.008 0.001 TYR J 65 ARG 0.001 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 1344) hydrogen bonds : angle 3.12427 ( 3996) SS BOND : bond 0.00056 ( 36) SS BOND : angle 0.43897 ( 72) covalent geometry : bond 0.00232 (17496) covalent geometry : angle 0.43886 (23904) *********************** 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 275 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 1.810 Fit side-chains REVERT: A 34 MET cc_start: 0.8807 (mmm) cc_final: 0.8327 (mtm) REVERT: A 93 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.7936 (mpp) REVERT: B 93 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8029 (mpp) REVERT: D 34 MET cc_start: 0.8961 (mmp) cc_final: 0.8401 (mtm) REVERT: D 93 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.7940 (mpp) REVERT: G 34 MET cc_start: 0.8806 (mmm) cc_final: 0.8331 (mtm) REVERT: G 93 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.7946 (mpp) REVERT: H 93 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8037 (mpp) REVERT: J 34 MET cc_start: 0.8799 (mmm) cc_final: 0.8327 (mtm) REVERT: J 93 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.7935 (mpp) REVERT: K 93 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8028 (mpp) REVERT: K 97 HIS cc_start: 0.8220 (t-90) cc_final: 0.7956 (t-170) outliers start: 55 outliers final: 15 residues processed: 266 average time/residue: 1.2773 time to fit residues: 379.1555 Evaluate side-chains 234 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 93 MET 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 93 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 64 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 HIS ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.073696 restraints weight = 24874.056| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.98 r_work: 0.2759 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17532 Z= 0.144 Angle : 0.476 4.858 23976 Z= 0.256 Chirality : 0.040 0.158 2856 Planarity : 0.004 0.043 2856 Dihedral : 3.700 14.203 2280 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.83 % Allowed : 21.33 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.16), residues: 2076 helix: 4.14 (0.10), residues: 1488 sheet: 1.66 (0.48), residues: 132 loop : -2.07 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 133 HIS 0.004 0.001 HIS I 97 PHE 0.011 0.002 PHE K 180 TYR 0.014 0.001 TYR B 65 ARG 0.002 0.000 ARG I 32 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 1344) hydrogen bonds : angle 3.19596 ( 3996) SS BOND : bond 0.00068 ( 36) SS BOND : angle 0.55210 ( 72) covalent geometry : bond 0.00345 (17496) covalent geometry : angle 0.47541 (23904) *********************** 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 276 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 222 time to evaluate : 2.389 Fit side-chains REVERT: A 34 MET cc_start: 0.8810 (mmm) cc_final: 0.8372 (mtm) REVERT: A 93 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.7961 (mpp) REVERT: C 156 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8908 (mp) REVERT: C 211 TYR cc_start: 0.8532 (t80) cc_final: 0.8325 (t80) REVERT: D 34 MET cc_start: 0.8971 (mmp) cc_final: 0.8427 (mtm) REVERT: D 93 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.7958 (mpp) REVERT: D 211 TYR cc_start: 0.8490 (t80) cc_final: 0.8250 (t80) REVERT: F 211 TYR cc_start: 0.8527 (t80) cc_final: 0.8326 (t80) REVERT: G 34 MET cc_start: 0.8821 (mmm) cc_final: 0.8375 (mtm) REVERT: G 93 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.7954 (mpp) REVERT: I 156 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8904 (mp) REVERT: I 211 TYR cc_start: 0.8534 (t80) cc_final: 0.8331 (t80) REVERT: J 34 MET cc_start: 0.8812 (mmm) cc_final: 0.8372 (mtm) REVERT: J 93 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.7963 (mpp) REVERT: K 97 HIS cc_start: 0.8249 (t-90) cc_final: 0.7964 (t-170) outliers start: 54 outliers final: 33 residues processed: 266 average time/residue: 1.6767 time to fit residues: 498.5181 Evaluate side-chains 257 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 25 LEU 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 156 LEU 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 23 VAL Chi-restraints excluded: chain E residue 25 LEU 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 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 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 LEU 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 143 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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** ** G 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** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.074747 restraints weight = 24769.241| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.99 r_work: 0.2791 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2344 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= 0.108 Angle : 0.453 4.763 23976 Z= 0.243 Chirality : 0.038 0.151 2856 Planarity : 0.003 0.041 2856 Dihedral : 3.602 14.475 2280 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.83 % Allowed : 22.75 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.37 (0.16), residues: 2076 helix: 4.29 (0.10), residues: 1488 sheet: 1.70 (0.49), residues: 132 loop : -2.09 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 132 HIS 0.004 0.001 HIS I 97 PHE 0.009 0.001 PHE E 180 TYR 0.008 0.001 TYR A 65 ARG 0.001 0.000 ARG I 32 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 1344) hydrogen bonds : angle 3.11411 ( 3996) SS BOND : bond 0.00059 ( 36) SS BOND : angle 0.47861 ( 72) covalent geometry : bond 0.00246 (17496) covalent geometry : angle 0.45327 (23904) *********************** 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 272 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 1.971 Fit side-chains REVERT: A 34 MET cc_start: 0.8833 (mmm) cc_final: 0.8358 (mtm) REVERT: A 93 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.7911 (mpp) REVERT: A 211 TYR cc_start: 0.8495 (t80) cc_final: 0.8271 (t80) REVERT: A 215 ARG cc_start: 0.7873 (mpt180) cc_final: 0.7619 (mpt180) REVERT: B 93 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8015 (mpp) REVERT: C 211 TYR cc_start: 0.8562 (t80) cc_final: 0.8351 (t80) REVERT: C 215 ARG cc_start: 0.7956 (mpt180) cc_final: 0.7741 (mmt90) REVERT: D 34 MET cc_start: 0.8988 (mmp) cc_final: 0.8430 (mtm) REVERT: D 93 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.7911 (mpp) REVERT: D 215 ARG cc_start: 0.7861 (mpt180) cc_final: 0.7656 (mmt90) REVERT: F 211 TYR cc_start: 0.8561 (t80) cc_final: 0.8356 (t80) REVERT: F 215 ARG cc_start: 0.7945 (mpt180) cc_final: 0.7730 (mmt90) REVERT: G 34 MET cc_start: 0.8816 (mmm) cc_final: 0.8352 (mtm) REVERT: G 93 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.7911 (mpp) REVERT: G 211 TYR cc_start: 0.8507 (t80) cc_final: 0.8286 (t80) REVERT: G 215 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7616 (mpt180) REVERT: I 211 TYR cc_start: 0.8565 (t80) cc_final: 0.8362 (t80) REVERT: I 215 ARG cc_start: 0.7954 (mpt180) cc_final: 0.7740 (mmt90) REVERT: J 34 MET cc_start: 0.8815 (mmm) cc_final: 0.8350 (mtm) REVERT: J 93 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.7903 (mpp) REVERT: J 215 ARG cc_start: 0.7873 (mpt180) cc_final: 0.7658 (mmt90) REVERT: K 97 HIS cc_start: 0.8265 (t-90) cc_final: 0.7977 (t-170) REVERT: L 215 ARG cc_start: 0.7963 (mpt180) cc_final: 0.7753 (mmt90) outliers start: 35 outliers final: 19 residues processed: 266 average time/residue: 1.3288 time to fit residues: 392.1948 Evaluate side-chains 250 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU 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 B residue 93 MET 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 E residue 23 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU 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 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 52 ILE 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 119 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 187 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 0.0270 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- 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** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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** ** J 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 = 0.3538 r_free = 0.3538 target = 0.107784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.073256 restraints weight = 24638.510| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.97 r_work: 0.2762 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: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17532 Z= 0.129 Angle : 0.475 4.933 23976 Z= 0.256 Chirality : 0.039 0.155 2856 Planarity : 0.003 0.040 2856 Dihedral : 3.612 14.140 2280 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.20 % Allowed : 23.27 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.16), residues: 2076 helix: 4.18 (0.10), residues: 1488 sheet: 1.76 (0.49), residues: 132 loop : -2.10 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 132 HIS 0.004 0.001 HIS L 97 PHE 0.012 0.002 PHE A 180 TYR 0.012 0.001 TYR J 65 ARG 0.002 0.000 ARG L 32 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 1344) hydrogen bonds : angle 3.13945 ( 3996) SS BOND : bond 0.00049 ( 36) SS BOND : angle 0.49878 ( 72) covalent geometry : bond 0.00305 (17496) covalent geometry : angle 0.47483 (23904) *********************** 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 268 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 2.053 Fit side-chains REVERT: A 34 MET cc_start: 0.8854 (mmm) cc_final: 0.8402 (mtm) REVERT: A 93 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.7885 (mpp) REVERT: B 93 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8011 (mpp) REVERT: B 215 ARG cc_start: 0.7898 (mpt180) cc_final: 0.7661 (mmt90) REVERT: D 34 MET cc_start: 0.9013 (mmp) cc_final: 0.8469 (mtm) REVERT: D 93 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.7901 (mpp) REVERT: D 211 TYR cc_start: 0.8493 (t80) cc_final: 0.8214 (t80) REVERT: E 97 HIS cc_start: 0.7966 (t-90) cc_final: 0.7727 (t-90) REVERT: E 215 ARG cc_start: 0.7926 (mpt180) cc_final: 0.7678 (mmt90) REVERT: G 34 MET cc_start: 0.8840 (mmm) cc_final: 0.8395 (mtm) REVERT: G 93 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.7904 (mpp) REVERT: H 215 ARG cc_start: 0.7914 (mpt180) cc_final: 0.7663 (mmt90) REVERT: J 34 MET cc_start: 0.8841 (mmm) cc_final: 0.8394 (mtm) REVERT: J 93 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.7882 (mpp) REVERT: J 211 TYR cc_start: 0.8455 (t80) cc_final: 0.8194 (t80) REVERT: K 97 HIS cc_start: 0.8267 (t-90) cc_final: 0.7977 (t-170) REVERT: K 215 ARG cc_start: 0.7921 (mpt180) cc_final: 0.7686 (mmt90) outliers start: 42 outliers final: 23 residues processed: 260 average time/residue: 1.3164 time to fit residues: 380.3517 Evaluate side-chains 254 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 93 MET 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 D residue 93 MET Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain F residue 23 VAL 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 23 VAL 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 23 VAL Chi-restraints excluded: chain K residue 52 ILE 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 20 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.072294 restraints weight = 24862.613| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.96 r_work: 0.2744 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2549 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= 0.144 Angle : 0.498 5.000 23976 Z= 0.268 Chirality : 0.040 0.153 2856 Planarity : 0.004 0.040 2856 Dihedral : 3.652 14.349 2280 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.83 % Allowed : 23.64 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.16), residues: 2076 helix: 4.11 (0.10), residues: 1488 sheet: 1.68 (0.49), residues: 132 loop : -2.07 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 133 HIS 0.004 0.001 HIS L 97 PHE 0.012 0.002 PHE D 180 TYR 0.013 0.001 TYR E 65 ARG 0.002 0.000 ARG F 215 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 1344) hydrogen bonds : angle 3.16480 ( 3996) SS BOND : bond 0.00071 ( 36) SS BOND : angle 0.56010 ( 72) covalent geometry : bond 0.00345 (17496) covalent geometry : angle 0.49730 (23904) *********************** 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 260 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 1.774 Fit side-chains REVERT: A 34 MET cc_start: 0.8861 (mmm) cc_final: 0.8421 (mtm) REVERT: A 93 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.7913 (mpp) REVERT: A 215 ARG cc_start: 0.7882 (mpt180) cc_final: 0.7638 (mmt90) REVERT: D 34 MET cc_start: 0.9024 (mmp) cc_final: 0.8468 (mtm) REVERT: D 93 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.7908 (mpp) REVERT: D 215 ARG cc_start: 0.7907 (mpt180) cc_final: 0.7589 (mmt90) REVERT: G 34 MET cc_start: 0.8852 (mmm) cc_final: 0.8421 (mtm) REVERT: G 93 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.7914 (mpp) REVERT: G 215 ARG cc_start: 0.7899 (mpt180) cc_final: 0.7656 (mmt90) REVERT: J 34 MET cc_start: 0.8843 (mmm) cc_final: 0.8412 (mtm) REVERT: J 215 ARG cc_start: 0.7881 (mpt180) cc_final: 0.7614 (mpt180) outliers start: 35 outliers final: 24 residues processed: 255 average time/residue: 1.3070 time to fit residues: 370.0131 Evaluate side-chains 252 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 23 VAL Chi-restraints excluded: chain D residue 18 THR 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 23 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain F residue 23 VAL 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 23 VAL 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 K residue 23 VAL Chi-restraints excluded: chain K residue 52 ILE 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 51 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** ** D 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 = 0.3510 r_free = 0.3510 target = 0.105670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.071175 restraints weight = 24804.531| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.95 r_work: 0.2727 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17532 Z= 0.173 Angle : 0.521 5.505 23976 Z= 0.282 Chirality : 0.041 0.155 2856 Planarity : 0.004 0.040 2856 Dihedral : 3.733 14.424 2280 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.68 % Allowed : 23.85 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.16), residues: 2076 helix: 3.95 (0.10), residues: 1488 sheet: 1.58 (0.49), residues: 132 loop : -2.05 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 133 HIS 0.005 0.001 HIS L 97 PHE 0.013 0.002 PHE E 180 TYR 0.015 0.002 TYR H 65 ARG 0.003 0.001 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 1344) hydrogen bonds : angle 3.25345 ( 3996) SS BOND : bond 0.00096 ( 36) SS BOND : angle 0.59156 ( 72) covalent geometry : bond 0.00421 (17496) covalent geometry : angle 0.52112 (23904) ********************** 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 257 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.933 Fit side-chains REVERT: A 34 MET cc_start: 0.8863 (mmm) cc_final: 0.8421 (mtm) REVERT: A 211 TYR cc_start: 0.8463 (t80) cc_final: 0.8167 (t80) REVERT: A 215 ARG cc_start: 0.7804 (mpt180) cc_final: 0.7598 (mmt90) REVERT: B 215 ARG cc_start: 0.7946 (mmt90) cc_final: 0.7714 (mmt90) REVERT: C 215 ARG cc_start: 0.7972 (mpt180) cc_final: 0.7726 (mmt90) REVERT: D 34 MET cc_start: 0.9036 (mmp) cc_final: 0.8469 (mtm) REVERT: D 211 TYR cc_start: 0.8488 (t80) cc_final: 0.8132 (t80) REVERT: D 215 ARG cc_start: 0.7854 (mpt180) cc_final: 0.7521 (mmt90) REVERT: F 215 ARG cc_start: 0.7968 (mpt180) cc_final: 0.7719 (mmt90) REVERT: G 34 MET cc_start: 0.8856 (mmm) cc_final: 0.8418 (mtm) REVERT: G 211 TYR cc_start: 0.8464 (t80) cc_final: 0.8171 (t80) REVERT: G 215 ARG cc_start: 0.7817 (mpt180) cc_final: 0.7608 (mmt90) REVERT: I 215 ARG cc_start: 0.7970 (mpt180) cc_final: 0.7724 (mmt90) REVERT: J 34 MET cc_start: 0.8856 (mmm) cc_final: 0.8414 (mtm) REVERT: J 215 ARG cc_start: 0.7903 (mpt180) cc_final: 0.7638 (mmt90) REVERT: K 215 ARG cc_start: 0.7962 (mmt90) cc_final: 0.7728 (mmt90) REVERT: L 215 ARG cc_start: 0.7973 (mpt180) cc_final: 0.7730 (mmt90) outliers start: 32 outliers final: 24 residues processed: 251 average time/residue: 1.3343 time to fit residues: 370.9180 Evaluate side-chains 249 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 18 THR 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 E residue 52 ILE Chi-restraints excluded: chain F residue 23 VAL 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 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 25 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 52 ILE 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 71 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 116 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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** ** J 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 = 0.3573 r_free = 0.3573 target = 0.109694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.076156 restraints weight = 25565.568| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.98 r_work: 0.2827 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17532 Z= 0.109 Angle : 0.472 5.114 23976 Z= 0.253 Chirality : 0.038 0.148 2856 Planarity : 0.003 0.039 2856 Dihedral : 3.572 14.376 2280 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.05 % Allowed : 24.95 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.26 (0.17), residues: 2076 helix: 4.22 (0.10), residues: 1488 sheet: 1.70 (0.49), residues: 132 loop : -2.18 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.004 0.001 HIS E 97 PHE 0.009 0.001 PHE E 180 TYR 0.007 0.001 TYR K 65 ARG 0.004 0.000 ARG C 22 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 1344) hydrogen bonds : angle 3.08504 ( 3996) SS BOND : bond 0.00043 ( 36) SS BOND : angle 0.50074 ( 72) covalent geometry : bond 0.00238 (17496) covalent geometry : angle 0.47162 (23904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13734.20 seconds wall clock time: 238 minutes 16.54 seconds (14296.54 seconds total)