Starting phenix.real_space_refine on Wed Jul 23 09:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yl0_33901/07_2025/7yl0_33901.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yl0_33901/07_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_33901/07_2025/7yl0_33901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yl0_33901/07_2025/7yl0_33901.map" model { file = "/net/cci-nas-00/data/ceres_data/7yl0_33901/07_2025/7yl0_33901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yl0_33901/07_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-5711/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: 2.37, per 1000 atoms: 0.80 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: 0.72 Conformation dependent library (CDL) restraints added in 328.1 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: 0.33 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: 0.57 Time building geometry restraints manager: 0.86 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: 0.740 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.810 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- 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 3000 Z= 1.083 Angle : 2.450 28.146 4080 Z= 1.508 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 Details of bonding type rmsd hydrogen bonds : bond 0.09405 ( 58) hydrogen bonds : angle 6.45202 ( 174) SS BOND : bond 0.02749 ( 6) SS BOND : angle 4.14910 ( 12) covalent geometry : bond 0.01469 ( 2994) covalent geometry : angle 2.44304 ( 4068) *********************** 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 : 0.330 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: 0.1622 time to fit residues: 23.7031 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: 6.9990 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 = 0.4364 r_free = 0.4364 target = 0.114996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.090480 restraints weight = 5086.336| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.05 r_work: 0.3899 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 3000 Z= 0.128 Angle : 0.659 7.612 4080 Z= 0.329 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 Details of bonding type rmsd hydrogen bonds : bond 0.01679 ( 58) hydrogen bonds : angle 4.78544 ( 174) SS BOND : bond 0.00461 ( 6) SS BOND : angle 1.69257 ( 12) covalent geometry : bond 0.00252 ( 2994) covalent geometry : angle 0.65316 ( 4068) *********************** 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 : 0.335 Fit side-chains REVERT: L 34 SER cc_start: 0.8461 (t) cc_final: 0.8162 (p) REVERT: A 7 CYS cc_start: 0.6031 (t) cc_final: 0.5624 (p) REVERT: A 27 LEU cc_start: 0.7686 (tt) cc_final: 0.7373 (mp) REVERT: D 27 LEU cc_start: 0.7841 (tt) cc_final: 0.7532 (mp) REVERT: D 34 SER cc_start: 0.8937 (p) cc_final: 0.8642 (m) REVERT: E 31 ASN cc_start: 0.8271 (m-40) cc_final: 0.8010 (m-40) REVERT: F 15 PHE cc_start: 0.8080 (m-80) cc_final: 0.6930 (p90) REVERT: K 10 GLN cc_start: 0.7288 (tt0) cc_final: 0.6409 (pm20) outliers start: 10 outliers final: 4 residues processed: 85 average time/residue: 0.1283 time to fit residues: 13.4021 Evaluate side-chains 69 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4515 r_free = 0.4515 target = 0.156171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.125207 restraints weight = 4646.520| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.24 r_work: 0.3792 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3000 Z= 0.166 Angle : 0.619 7.189 4080 Z= 0.316 Chirality : 0.042 0.136 492 Planarity : 0.002 0.011 534 Dihedral : 9.084 32.164 480 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.78 % Allowed : 16.05 % Favored : 81.17 % 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: -4.73 (0.27), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.20), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 18 PHE 0.017 0.002 PHE I 23 ARG 0.003 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.01652 ( 58) hydrogen bonds : angle 4.04124 ( 174) SS BOND : bond 0.00489 ( 6) SS BOND : angle 0.98641 ( 12) covalent geometry : bond 0.00331 ( 2994) covalent geometry : angle 0.61774 ( 4068) *********************** 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 70 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.328 Fit side-chains REVERT: L 34 SER cc_start: 0.8452 (t) cc_final: 0.8080 (m) REVERT: A 34 SER cc_start: 0.8841 (p) cc_final: 0.8427 (m) REVERT: B 27 LEU cc_start: 0.7698 (tt) cc_final: 0.7300 (mp) REVERT: D 34 SER cc_start: 0.8930 (p) cc_final: 0.8616 (m) REVERT: F 34 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8330 (m) REVERT: K 10 GLN cc_start: 0.7151 (tt0) cc_final: 0.6238 (tm-30) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.1302 time to fit residues: 10.1869 Evaluate side-chains 58 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 12 LEU 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 Chi-restraints excluded: chain F residue 34 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.0050 chunk 6 optimal weight: 0.3980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4567 r_free = 0.4567 target = 0.159325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.128352 restraints weight = 4651.570| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.42 r_work: 0.4396 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.4319 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3000 Z= 0.116 Angle : 0.588 6.319 4080 Z= 0.296 Chirality : 0.040 0.123 492 Planarity : 0.002 0.010 534 Dihedral : 6.562 21.895 480 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.47 % Allowed : 17.90 % 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: -4.70 (0.27), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 18 PHE 0.016 0.002 PHE B 23 ARG 0.001 0.000 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.01367 ( 58) hydrogen bonds : angle 3.71605 ( 174) SS BOND : bond 0.00582 ( 6) SS BOND : angle 1.51250 ( 12) covalent geometry : bond 0.00241 ( 2994) covalent geometry : angle 0.58324 ( 4068) *********************** 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 70 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.339 Fit side-chains REVERT: F 15 PHE cc_start: 0.7463 (m-80) cc_final: 0.6592 (p90) REVERT: K 10 GLN cc_start: 0.6729 (tt0) cc_final: 0.6505 (tm-30) outliers start: 8 outliers final: 7 residues processed: 66 average time/residue: 0.1051 time to fit residues: 8.9436 Evaluate side-chains 56 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 CYS Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain C residue 12 LEU 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 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: 1.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN K 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.156812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.125431 restraints weight = 4654.289| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.23 r_work: 0.3870 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3000 Z= 0.170 Angle : 0.601 6.303 4080 Z= 0.306 Chirality : 0.041 0.133 492 Planarity : 0.002 0.014 534 Dihedral : 9.182 33.423 480 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.09 % Allowed : 16.05 % Favored : 80.86 % 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: -4.64 (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 0.004 0.001 HIS H 18 PHE 0.017 0.002 PHE B 23 ARG 0.001 0.000 ARG L 11 Details of bonding type rmsd hydrogen bonds : bond 0.01569 ( 58) hydrogen bonds : angle 3.60086 ( 174) SS BOND : bond 0.00555 ( 6) SS BOND : angle 1.22710 ( 12) covalent geometry : bond 0.00342 ( 2994) covalent geometry : angle 0.59827 ( 4068) *********************** 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 63 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.312 Fit side-chains REVERT: B 15 PHE cc_start: 0.8045 (m-80) cc_final: 0.7640 (m-80) REVERT: K 10 GLN cc_start: 0.7127 (tt0) cc_final: 0.6430 (tm-30) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.1134 time to fit residues: 8.5773 Evaluate side-chains 57 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 CYS Chi-restraints excluded: chain A 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 12 LEU 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: 3.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN C 22 ASN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** F 22 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 = 0.4499 r_free = 0.4499 target = 0.153468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.121450 restraints weight = 4831.711| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.26 r_work: 0.3823 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.6585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3000 Z= 0.232 Angle : 0.643 8.347 4080 Z= 0.329 Chirality : 0.042 0.134 492 Planarity : 0.003 0.017 534 Dihedral : 14.619 59.820 480 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.78 % Allowed : 16.98 % Favored : 80.25 % 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: -4.54 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 18 PHE 0.018 0.003 PHE B 23 ARG 0.003 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.01771 ( 58) hydrogen bonds : angle 3.68198 ( 174) SS BOND : bond 0.00538 ( 6) SS BOND : angle 1.37285 ( 12) covalent geometry : bond 0.00456 ( 2994) covalent geometry : angle 0.63984 ( 4068) *********************** 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: 9 poor density : 46 time to evaluate : 0.333 Fit side-chains REVERT: B 15 PHE cc_start: 0.7964 (m-80) cc_final: 0.7497 (m-80) REVERT: F 15 PHE cc_start: 0.7865 (m-80) cc_final: 0.6623 (p90) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.1076 time to fit residues: 7.0362 Evaluate side-chains 48 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 CYS Chi-restraints excluded: chain A 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 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: 8.9990 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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 = 0.4560 r_free = 0.4560 target = 0.159168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.127422 restraints weight = 4661.612| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.24 r_work: 0.3911 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3000 Z= 0.123 Angle : 0.590 8.990 4080 Z= 0.288 Chirality : 0.040 0.127 492 Planarity : 0.002 0.008 534 Dihedral : 10.479 56.372 480 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.47 % Allowed : 18.21 % Favored : 79.32 % 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: -4.58 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.019 0.002 PHE B 23 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.01464 ( 58) hydrogen bonds : angle 3.50542 ( 174) SS BOND : bond 0.00475 ( 6) SS BOND : angle 1.00352 ( 12) covalent geometry : bond 0.00254 ( 2994) covalent geometry : angle 0.58856 ( 4068) *********************** 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: 8 poor density : 49 time to evaluate : 0.304 Fit side-chains REVERT: C 15 PHE cc_start: 0.7725 (m-80) cc_final: 0.6421 (p90) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.1050 time to fit residues: 7.1249 Evaluate side-chains 51 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 6 THR 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: 9.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS ** F 22 ASN ** 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 = 0.4432 r_free = 0.4432 target = 0.147318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.114968 restraints weight = 4917.095| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.16 r_work: 0.3748 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 3000 Z= 0.394 Angle : 0.764 8.977 4080 Z= 0.405 Chirality : 0.048 0.152 492 Planarity : 0.004 0.017 534 Dihedral : 17.829 59.812 480 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 2.78 % Allowed : 17.59 % 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: -4.48 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS J 18 PHE 0.026 0.004 PHE I 15 ARG 0.005 0.001 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.02285 ( 58) hydrogen bonds : angle 4.03938 ( 174) SS BOND : bond 0.00579 ( 6) SS BOND : angle 1.47686 ( 12) covalent geometry : bond 0.00772 ( 2994) covalent geometry : angle 0.76067 ( 4068) *********************** 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 54 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.356 Fit side-chains REVERT: B 15 PHE cc_start: 0.7724 (m-80) cc_final: 0.7313 (m-80) REVERT: D 27 LEU cc_start: 0.7712 (tt) cc_final: 0.7271 (mp) REVERT: F 15 PHE cc_start: 0.7994 (m-80) cc_final: 0.6837 (p90) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.1193 time to fit residues: 7.1627 Evaluate side-chains 51 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B 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 6 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: 5.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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 = 0.152162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.119884 restraints weight = 4849.148| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.22 r_work: 0.3751 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3000 Z= 0.198 Angle : 0.636 9.485 4080 Z= 0.321 Chirality : 0.042 0.133 492 Planarity : 0.002 0.009 534 Dihedral : 15.791 59.895 480 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.78 % Allowed : 18.52 % Favored : 78.70 % 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: -4.52 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 18 PHE 0.018 0.002 PHE D 23 ARG 0.003 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.01802 ( 58) hydrogen bonds : angle 3.83416 ( 174) SS BOND : bond 0.00347 ( 6) SS BOND : angle 1.03422 ( 12) covalent geometry : bond 0.00381 ( 2994) covalent geometry : angle 0.63422 ( 4068) *********************** 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 55 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.313 Fit side-chains REVERT: B 15 PHE cc_start: 0.7469 (m-80) cc_final: 0.6947 (m-80) REVERT: C 15 PHE cc_start: 0.7915 (m-80) cc_final: 0.6582 (p90) REVERT: D 27 LEU cc_start: 0.7564 (tt) cc_final: 0.7121 (mp) REVERT: K 11 ARG cc_start: 0.5566 (mmp-170) cc_final: 0.5059 (mmm160) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.1377 time to fit residues: 8.4997 Evaluate side-chains 49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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: 6.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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 = 0.4456 r_free = 0.4456 target = 0.149502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.117164 restraints weight = 4870.634| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.20 r_work: 0.3780 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.7161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3000 Z= 0.265 Angle : 0.678 9.440 4080 Z= 0.349 Chirality : 0.044 0.140 492 Planarity : 0.003 0.010 534 Dihedral : 15.778 59.513 480 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % 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: -4.52 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 18 PHE 0.018 0.003 PHE B 23 ARG 0.004 0.001 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.02015 ( 58) hydrogen bonds : angle 3.99122 ( 174) SS BOND : bond 0.00435 ( 6) SS BOND : angle 1.13568 ( 12) covalent geometry : bond 0.00512 ( 2994) covalent geometry : angle 0.67599 ( 4068) ********************** 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 55 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.308 Fit side-chains REVERT: B 15 PHE cc_start: 0.7590 (m-80) cc_final: 0.7140 (m-80) REVERT: C 15 PHE cc_start: 0.7990 (m-80) cc_final: 0.6686 (p90) REVERT: D 27 LEU cc_start: 0.7695 (tt) cc_final: 0.7281 (mp) REVERT: K 11 ARG cc_start: 0.5655 (mmp-170) cc_final: 0.5155 (mmm160) outliers start: 8 outliers final: 8 residues processed: 49 average time/residue: 0.1157 time to fit residues: 7.2164 Evaluate side-chains 53 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B 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 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 21 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 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 = 0.4511 r_free = 0.4511 target = 0.154225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.122493 restraints weight = 4700.369| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.18 r_work: 0.3863 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.7258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3000 Z= 0.144 Angle : 0.602 9.636 4080 Z= 0.299 Chirality : 0.041 0.126 492 Planarity : 0.002 0.008 534 Dihedral : 13.537 56.295 480 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.16 % Allowed : 20.68 % 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: -4.50 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.018 0.002 PHE B 23 ARG 0.002 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.01655 ( 58) hydrogen bonds : angle 3.76434 ( 174) SS BOND : bond 0.00299 ( 6) SS BOND : angle 0.81390 ( 12) covalent geometry : bond 0.00279 ( 2994) covalent geometry : angle 0.60109 ( 4068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.78 seconds wall clock time: 38 minutes 30.93 seconds (2310.93 seconds total)