Starting phenix.real_space_refine on Mon Feb 10 22:01:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yl0_33901/02_2025/7yl0_33901.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yl0_33901/02_2025/7yl0_33901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yl0_33901/02_2025/7yl0_33901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yl0_33901/02_2025/7yl0_33901.map" model { file = "/net/cci-nas-00/data/ceres_data/7yl0_33901/02_2025/7yl0_33901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yl0_33901/02_2025/7yl0_33901.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 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 12 5.16 5 C 1800 2.51 5 N 552 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2958 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "B" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "C" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "D" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "F" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "K" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Time building chain proxies: 2.51, per 1000 atoms: 0.85 Number of scatterers: 2958 At special positions: 0 Unit cell: (142.48, 85.28, 42.64, 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 12 16.00 O 594 8.00 N 552 7.00 C 1800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 2 " - pdb=" SG CYS A 7 " distance=2.08 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 7 " distance=2.02 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 7 " distance=2.06 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 7 " distance=2.06 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.06 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: 0.74 Conformation dependent library (CDL) restraints added in 269.1 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 54.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 10 through 22 removed outlier: 6.299A pdb=" N GLN H 10 " --> pdb=" O ARG J 11 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA J 13 " --> pdb=" O GLN H 10 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU H 12 " --> pdb=" O ALA J 13 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE J 15 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN H 14 " --> pdb=" O PHE J 15 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL J 17 " --> pdb=" O ASN H 14 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU H 16 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER J 19 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N HIS H 18 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN J 21 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER H 20 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN J 10 " --> pdb=" O ARG L 11 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA L 13 " --> pdb=" O GLN J 10 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU J 12 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE L 15 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN J 14 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL L 17 " --> pdb=" O ASN J 14 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU J 16 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N SER L 19 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS J 18 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASN L 21 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER J 20 " --> pdb=" O ASN L 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 25 through 30 Processing sheet with id=AA3, first strand: chain 'B' and resid 7 through 21 removed outlier: 6.450A pdb=" N CYS A 7 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLN C 10 " --> pdb=" O CYS A 7 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR A 9 " --> pdb=" O GLN C 10 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU C 12 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ARG A 11 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN C 14 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA A 13 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU C 16 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A 15 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N HIS C 18 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL A 17 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N SER C 20 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER A 19 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 30 removed outlier: 6.379A pdb=" N LEU A 27 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N THR C 30 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER A 29 " --> pdb=" O THR C 30 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.409A pdb=" N ASN A 35 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 21 removed outlier: 6.439A pdb=" N CYS D 7 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLN F 10 " --> pdb=" O CYS D 7 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR D 9 " --> pdb=" O GLN F 10 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU F 12 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ARG D 11 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASN F 14 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA D 13 " --> pdb=" O ASN F 14 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU F 16 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE D 15 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N HIS F 18 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL D 17 " --> pdb=" O HIS F 18 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER F 20 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER D 19 " --> pdb=" O SER F 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 26 through 30 removed outlier: 6.379A pdb=" N LEU D 27 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N THR F 30 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER D 29 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.408A pdb=" N ASN D 35 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 22 removed outlier: 6.300A pdb=" N GLN G 10 " --> pdb=" O ARG I 11 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA I 13 " --> pdb=" O GLN G 10 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU G 12 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE I 15 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASN G 14 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL I 17 " --> pdb=" O ASN G 14 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU G 16 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N SER I 19 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N HIS G 18 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN I 21 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER G 20 " --> pdb=" O ASN I 21 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN I 10 " --> pdb=" O ARG K 11 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA K 13 " --> pdb=" O GLN I 10 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU I 12 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE K 15 " --> pdb=" O LEU I 12 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN I 14 " --> pdb=" O PHE K 15 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL K 17 " --> pdb=" O ASN I 14 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU I 16 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N SER K 19 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS I 18 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ASN K 21 " --> pdb=" O HIS I 18 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER I 20 " --> pdb=" O ASN K 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 25 through 30 58 hydrogen bonds defined for protein. 174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 597 1.32 - 1.46: 1114 1.46 - 1.59: 1271 1.59 - 1.73: 0 1.73 - 1.87: 12 Bond restraints: 2994 Sorted by residual: bond pdb=" C THR K 36 " pdb=" N TYC K 37 " ideal model delta sigma weight residual 1.329 1.200 0.129 1.40e-02 5.10e+03 8.46e+01 bond pdb=" C THR H 36 " pdb=" N TYC H 37 " ideal model delta sigma weight residual 1.329 1.201 0.128 1.40e-02 5.10e+03 8.40e+01 bond pdb=" C THR G 36 " pdb=" N TYC G 37 " ideal model delta sigma weight residual 1.329 1.201 0.128 1.40e-02 5.10e+03 8.39e+01 bond pdb=" C THR J 36 " pdb=" N TYC J 37 " ideal model delta sigma weight residual 1.329 1.201 0.128 1.40e-02 5.10e+03 8.37e+01 bond pdb=" C THR L 36 " pdb=" N TYC L 37 " ideal model delta sigma weight residual 1.329 1.201 0.128 1.40e-02 5.10e+03 8.35e+01 ... (remaining 2989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.63: 3999 5.63 - 11.26: 45 11.26 - 16.89: 6 16.89 - 22.52: 12 22.52 - 28.15: 6 Bond angle restraints: 4068 Sorted by residual: angle pdb=" C THR F 36 " pdb=" N TYC F 37 " pdb=" CA TYC F 37 " ideal model delta sigma weight residual 121.70 149.85 -28.15 1.80e+00 3.09e-01 2.44e+02 angle pdb=" C THR D 36 " pdb=" N TYC D 37 " pdb=" CA TYC D 37 " ideal model delta sigma weight residual 121.70 149.81 -28.11 1.80e+00 3.09e-01 2.44e+02 angle pdb=" C THR C 36 " pdb=" N TYC C 37 " pdb=" CA TYC C 37 " ideal model delta sigma weight residual 121.70 149.77 -28.07 1.80e+00 3.09e-01 2.43e+02 angle pdb=" C THR E 36 " pdb=" N TYC E 37 " pdb=" CA TYC E 37 " ideal model delta sigma weight residual 121.70 149.74 -28.04 1.80e+00 3.09e-01 2.43e+02 angle pdb=" C THR A 36 " pdb=" N TYC A 37 " pdb=" CA TYC A 37 " ideal model delta sigma weight residual 121.70 149.73 -28.03 1.80e+00 3.09e-01 2.43e+02 ... (remaining 4063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 1692 17.09 - 34.18: 35 34.18 - 51.27: 43 51.27 - 68.35: 19 68.35 - 85.44: 5 Dihedral angle restraints: 1794 sinusoidal: 666 harmonic: 1128 Sorted by residual: dihedral pdb=" CB CYS A 2 " pdb=" SG CYS A 2 " pdb=" SG CYS A 7 " pdb=" CB CYS A 7 " ideal model delta sinusoidal sigma weight residual 93.00 7.56 85.44 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS E 2 " pdb=" SG CYS E 2 " pdb=" SG CYS E 7 " pdb=" CB CYS E 7 " ideal model delta sinusoidal sigma weight residual 93.00 8.56 84.44 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS D 2 " pdb=" SG CYS D 2 " pdb=" SG CYS D 7 " pdb=" CB CYS D 7 " ideal model delta sinusoidal sigma weight residual 93.00 9.95 83.05 1 1.00e+01 1.00e-02 8.44e+01 ... (remaining 1791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 263 0.065 - 0.130: 154 0.130 - 0.195: 39 0.195 - 0.261: 6 0.261 - 0.326: 30 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA VAL L 32 " pdb=" N VAL L 32 " pdb=" C VAL L 32 " pdb=" CB VAL L 32 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA VAL K 32 " pdb=" N VAL K 32 " pdb=" C VAL K 32 " pdb=" CB VAL K 32 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 489 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 36 " 0.017 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C THR E 36 " -0.049 2.00e-02 2.50e+03 pdb=" O THR E 36 " 0.014 2.00e-02 2.50e+03 pdb=" N TYC E 37 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 36 " 0.017 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C THR F 36 " -0.049 2.00e-02 2.50e+03 pdb=" O THR F 36 " 0.014 2.00e-02 2.50e+03 pdb=" N TYC F 37 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 36 " -0.017 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C THR B 36 " 0.049 2.00e-02 2.50e+03 pdb=" O THR B 36 " -0.014 2.00e-02 2.50e+03 pdb=" N TYC B 37 " -0.018 2.00e-02 2.50e+03 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 1753 2.99 - 3.47: 2611 3.47 - 3.95: 4484 3.95 - 4.42: 5081 4.42 - 4.90: 9391 Nonbonded interactions: 23320 Sorted by model distance: nonbonded pdb=" O THR K 36 " pdb=" CA TYC K 37 " model vdw 2.515 2.776 nonbonded pdb=" O THR J 36 " pdb=" CA TYC J 37 " model vdw 2.515 2.776 nonbonded pdb=" O THR I 36 " pdb=" CA TYC I 37 " model vdw 2.516 2.776 nonbonded pdb=" O THR L 36 " pdb=" CA TYC L 37 " model vdw 2.516 2.776 nonbonded pdb=" O THR H 36 " pdb=" CA TYC H 37 " model vdw 2.516 2.776 ... (remaining 23315 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.600 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.015 0.129 2994 Z= 0.998 Angle : 2.443 28.146 4068 Z= 1.506 Chirality : 0.107 0.326 492 Planarity : 0.005 0.029 534 Dihedral : 14.132 60.742 1032 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 18 PHE 0.027 0.005 PHE K 15 ARG 0.001 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 1 LYS cc_start: 0.5669 (mttt) cc_final: 0.5385 (tttt) REVERT: D 1 LYS cc_start: 0.5886 (mttt) cc_final: 0.5414 (tttt) REVERT: D 7 CYS cc_start: 0.6137 (t) cc_final: 0.5759 (p) REVERT: D 27 LEU cc_start: 0.7326 (tt) cc_final: 0.6989 (mp) REVERT: F 7 CYS cc_start: 0.3823 (t) cc_final: 0.3178 (t) REVERT: K 10 GLN cc_start: 0.6854 (tt0) cc_final: 0.6434 (pm20) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1703 time to fit residues: 24.8237 Evaluate side-chains 70 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.0270 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS H 22 ASN H 31 ASN J 14 ASN J 18 HIS J 22 ASN J 31 ASN L 14 ASN L 22 ASN L 31 ASN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 ASN G 31 ASN I 14 ASN I 22 ASN I 31 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 ASN K 18 HIS K 22 ASN K 31 ASN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.162051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.132670 restraints weight = 4599.342| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.33 r_work: 0.3980 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2994 Z= 0.167 Angle : 0.653 7.612 4068 Z= 0.327 Chirality : 0.043 0.129 492 Planarity : 0.002 0.011 534 Dihedral : 6.434 19.264 480 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.09 % Allowed : 14.81 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.27), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 18 PHE 0.013 0.002 PHE A 15 ARG 0.001 0.000 ARG E 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.328 Fit side-chains REVERT: L 34 SER cc_start: 0.8297 (t) cc_final: 0.8065 (p) REVERT: A 27 LEU cc_start: 0.7732 (tt) cc_final: 0.7452 (mp) REVERT: D 27 LEU cc_start: 0.7865 (tt) cc_final: 0.7588 (mp) REVERT: D 34 SER cc_start: 0.8870 (p) cc_final: 0.8594 (m) REVERT: E 31 ASN cc_start: 0.8323 (m-40) cc_final: 0.8075 (m-40) REVERT: F 15 PHE cc_start: 0.8015 (m-80) cc_final: 0.6915 (p90) REVERT: K 10 GLN cc_start: 0.7291 (tt0) cc_final: 0.6436 (pm20) outliers start: 10 outliers final: 4 residues processed: 85 average time/residue: 0.1277 time to fit residues: 13.2616 Evaluate side-chains 68 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain D residue 2 CYS Chi-restraints excluded: chain F residue 34 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN C 22 ASN D 22 ASN E 22 ASN F 18 HIS F 22 ASN I 18 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.103271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.081320 restraints weight = 5472.554| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.95 r_work: 0.3722 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2994 Z= 0.429 Angle : 0.735 6.655 4068 Z= 0.396 Chirality : 0.048 0.151 492 Planarity : 0.003 0.019 534 Dihedral : 17.406 59.886 480 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.70 % Allowed : 15.74 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.27), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS H 18 PHE 0.019 0.003 PHE I 15 ARG 0.004 0.001 ARG K 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.366 Fit side-chains REVERT: L 34 SER cc_start: 0.8578 (t) cc_final: 0.8362 (m) REVERT: A 34 SER cc_start: 0.8887 (p) cc_final: 0.8441 (m) REVERT: B 27 LEU cc_start: 0.7589 (tt) cc_final: 0.7147 (mp) REVERT: D 27 LEU cc_start: 0.7775 (tt) cc_final: 0.7343 (mp) REVERT: D 34 SER cc_start: 0.9001 (p) cc_final: 0.8645 (m) REVERT: K 10 GLN cc_start: 0.7257 (tt0) cc_final: 0.6484 (tm-30) outliers start: 12 outliers final: 9 residues processed: 56 average time/residue: 0.1373 time to fit residues: 9.5528 Evaluate side-chains 51 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 2 CYS Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 32 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.0270 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** 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 = 0.4512 r_free = 0.4512 target = 0.154612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.123695 restraints weight = 4797.807| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.26 r_work: 0.4343 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.4274 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2994 Z= 0.193 Angle : 0.618 6.952 4068 Z= 0.317 Chirality : 0.041 0.128 492 Planarity : 0.002 0.011 534 Dihedral : 14.539 59.563 480 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.85 % Allowed : 17.59 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.27), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 18 PHE 0.015 0.002 PHE B 23 ARG 0.002 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.322 Fit side-chains REVERT: A 1 LYS cc_start: 0.7017 (mmmt) cc_final: 0.6745 (mmmt) REVERT: K 10 GLN cc_start: 0.6819 (tt0) cc_final: 0.6570 (tm-30) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.1279 time to fit residues: 8.8395 Evaluate side-chains 48 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 32 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 0.2980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN B 18 HIS C 18 HIS G 18 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.149021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.116919 restraints weight = 4882.495| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.23 r_work: 0.3775 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2994 Z= 0.382 Angle : 0.696 7.013 4068 Z= 0.368 Chirality : 0.045 0.142 492 Planarity : 0.003 0.015 534 Dihedral : 16.523 59.583 480 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.70 % Allowed : 16.67 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 18 PHE 0.020 0.003 PHE C 23 ARG 0.003 0.001 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.335 Fit side-chains REVERT: B 15 PHE cc_start: 0.8106 (m-80) cc_final: 0.7748 (m-80) REVERT: F 15 PHE cc_start: 0.8041 (m-80) cc_final: 0.6662 (p90) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.1098 time to fit residues: 6.8579 Evaluate side-chains 49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 32 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS E 18 HIS K 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.148066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.115806 restraints weight = 4977.703| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.20 r_work: 0.3760 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2994 Z= 0.377 Angle : 0.708 8.493 4068 Z= 0.373 Chirality : 0.044 0.138 492 Planarity : 0.003 0.011 534 Dihedral : 16.075 59.518 480 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.09 % Allowed : 19.75 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS H 18 PHE 0.020 0.003 PHE C 23 ARG 0.003 0.001 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.310 Fit side-chains REVERT: B 15 PHE cc_start: 0.7962 (m-80) cc_final: 0.7544 (m-80) REVERT: F 15 PHE cc_start: 0.7911 (m-80) cc_final: 0.6688 (p90) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.1038 time to fit residues: 6.7100 Evaluate side-chains 47 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 32 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** 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 = 0.4527 r_free = 0.4527 target = 0.154843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.123041 restraints weight = 4766.971| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.28 r_work: 0.3878 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2994 Z= 0.158 Angle : 0.596 9.309 4068 Z= 0.297 Chirality : 0.041 0.123 492 Planarity : 0.002 0.008 534 Dihedral : 12.470 57.080 480 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.09 % Allowed : 19.44 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.016 0.002 PHE C 23 ARG 0.002 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.357 Fit side-chains REVERT: K 19 SER cc_start: 0.8431 (t) cc_final: 0.8145 (m) REVERT: K 34 SER cc_start: 0.8794 (t) cc_final: 0.8403 (m) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.1055 time to fit residues: 7.2607 Evaluate side-chains 48 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 32 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** 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 = 0.4487 r_free = 0.4487 target = 0.150621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.118085 restraints weight = 4811.596| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.20 r_work: 0.3796 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.7303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2994 Z= 0.258 Angle : 0.609 7.312 4068 Z= 0.319 Chirality : 0.042 0.134 492 Planarity : 0.002 0.008 534 Dihedral : 13.992 58.592 480 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.16 % Allowed : 18.83 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 18 PHE 0.017 0.002 PHE C 23 ARG 0.002 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.374 Fit side-chains REVERT: B 15 PHE cc_start: 0.7556 (m-80) cc_final: 0.7084 (m-80) REVERT: C 15 PHE cc_start: 0.7895 (m-80) cc_final: 0.6611 (p90) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.1079 time to fit residues: 5.8803 Evaluate side-chains 45 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 32 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** 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 = 0.4445 r_free = 0.4445 target = 0.147239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.116894 restraints weight = 4980.598| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.94 r_work: 0.3740 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2994 Z= 0.392 Angle : 0.685 7.523 4068 Z= 0.364 Chirality : 0.045 0.141 492 Planarity : 0.003 0.011 534 Dihedral : 15.972 59.420 480 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 2.47 % Allowed : 19.44 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 18 PHE 0.019 0.003 PHE C 23 ARG 0.004 0.001 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.306 Fit side-chains REVERT: B 15 PHE cc_start: 0.7650 (m-80) cc_final: 0.7224 (m-80) REVERT: F 15 PHE cc_start: 0.7927 (m-80) cc_final: 0.6736 (p90) outliers start: 8 outliers final: 7 residues processed: 43 average time/residue: 0.1157 time to fit residues: 6.4507 Evaluate side-chains 46 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** 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 = 0.4480 r_free = 0.4480 target = 0.150014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.119772 restraints weight = 4854.352| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.87 r_work: 0.3798 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.7523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2994 Z= 0.226 Angle : 0.629 9.142 4068 Z= 0.321 Chirality : 0.042 0.129 492 Planarity : 0.002 0.007 534 Dihedral : 14.445 57.812 480 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 1.85 % Allowed : 20.37 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 18 PHE 0.017 0.002 PHE C 23 ARG 0.003 0.000 ARG F 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.319 Fit side-chains REVERT: B 15 PHE cc_start: 0.7515 (m-80) cc_final: 0.7118 (m-80) REVERT: C 15 PHE cc_start: 0.7928 (m-80) cc_final: 0.6613 (p90) REVERT: K 34 SER cc_start: 0.8855 (t) cc_final: 0.8529 (m) outliers start: 6 outliers final: 6 residues processed: 44 average time/residue: 0.1178 time to fit residues: 6.6595 Evaluate side-chains 47 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 35 ASN ** 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 = 0.4450 r_free = 0.4450 target = 0.147319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.114272 restraints weight = 4871.712| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.19 r_work: 0.3764 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2994 Z= 0.367 Angle : 0.697 8.851 4068 Z= 0.364 Chirality : 0.044 0.140 492 Planarity : 0.003 0.011 534 Dihedral : 15.606 59.951 480 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 2.16 % Allowed : 20.37 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 18 PHE 0.019 0.003 PHE C 23 ARG 0.005 0.001 ARG F 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2027.09 seconds wall clock time: 36 minutes 34.17 seconds (2194.17 seconds total)