Starting phenix.real_space_refine on Mon Sep 23 13:08:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/09_2024/7yl0_33901.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/09_2024/7yl0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/09_2024/7yl0_33901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/09_2024/7yl0_33901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/09_2024/7yl0_33901.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl0_33901/09_2024/7yl0_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-5461/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: 2.54, per 1000 atoms: 0.86 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: 0.69 Conformation dependent library (CDL) restraints added in 325.1 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: 0.36 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: 0.83 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.110 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.150 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.340 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: 0.1645 time to fit residues: 24.0358 Evaluate side-chains 70 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.330 Fit side-chains REVERT: L 34 SER cc_start: 0.8109 (t) cc_final: 0.7853 (p) REVERT: A 7 CYS cc_start: 0.5302 (t) cc_final: 0.4980 (p) REVERT: A 27 LEU cc_start: 0.7286 (tt) cc_final: 0.6997 (mp) REVERT: D 27 LEU cc_start: 0.7479 (tt) cc_final: 0.7198 (mp) REVERT: D 34 SER cc_start: 0.8777 (p) cc_final: 0.8501 (m) REVERT: E 31 ASN cc_start: 0.8045 (m-40) cc_final: 0.7777 (m-40) REVERT: F 15 PHE cc_start: 0.7876 (m-80) cc_final: 0.6826 (p90) REVERT: K 10 GLN cc_start: 0.7387 (tt0) cc_final: 0.6470 (pm20) outliers start: 10 outliers final: 4 residues processed: 85 average time/residue: 0.1211 time to fit residues: 12.6868 Evaluate side-chains 69 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 22 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 ** 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2994 Z= 0.285 Angle : 0.652 7.071 4068 Z= 0.338 Chirality : 0.043 0.140 492 Planarity : 0.002 0.013 534 Dihedral : 11.581 39.974 480 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.09 % Allowed : 16.67 % 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: -4.71 (0.27), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.20), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 18 PHE 0.017 0.003 PHE I 23 ARG 0.003 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 69 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.304 Fit side-chains REVERT: L 34 SER cc_start: 0.8112 (t) cc_final: 0.7805 (m) REVERT: A 34 SER cc_start: 0.8728 (p) cc_final: 0.8339 (m) REVERT: B 27 LEU cc_start: 0.7311 (tt) cc_final: 0.6889 (mp) REVERT: D 34 SER cc_start: 0.8778 (p) cc_final: 0.8504 (m) REVERT: F 34 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8330 (m) REVERT: K 10 GLN cc_start: 0.7242 (tt0) cc_final: 0.6312 (tm-30) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.1245 time to fit residues: 9.5478 Evaluate side-chains 56 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 4 THR 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 3 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2994 Z= 0.205 Angle : 0.603 6.567 4068 Z= 0.308 Chirality : 0.041 0.130 492 Planarity : 0.002 0.011 534 Dihedral : 10.205 42.331 480 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.78 % Allowed : 17.90 % 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: -4.70 (0.27), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.20), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 18 PHE 0.016 0.002 PHE B 23 ARG 0.002 0.000 ARG F 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 65 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.335 Fit side-chains REVERT: L 34 SER cc_start: 0.8179 (t) cc_final: 0.7964 (m) REVERT: B 27 LEU cc_start: 0.7424 (tt) cc_final: 0.7003 (mp) REVERT: D 34 SER cc_start: 0.8838 (p) cc_final: 0.8535 (m) REVERT: F 15 PHE cc_start: 0.7797 (m-80) cc_final: 0.6649 (p90) REVERT: K 10 GLN cc_start: 0.7100 (tt0) cc_final: 0.6351 (tm-30) outliers start: 9 outliers final: 7 residues processed: 60 average time/residue: 0.1229 time to fit residues: 9.2353 Evaluate side-chains 55 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 2 CYS 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 21 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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 18 HIS C 18 HIS ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS D 22 ASN E 18 HIS E 22 ASN F 18 HIS F 22 ASN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 2994 Z= 0.550 Angle : 0.774 6.541 4068 Z= 0.421 Chirality : 0.049 0.151 492 Planarity : 0.004 0.019 534 Dihedral : 17.743 59.784 480 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 5.25 % Allowed : 15.43 % 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: -4.56 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS J 18 PHE 0.026 0.004 PHE I 15 ARG 0.004 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 66 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 49 time to evaluate : 0.332 Fit side-chains REVERT: A 27 LEU cc_start: 0.7270 (tt) cc_final: 0.6981 (mp) REVERT: B 15 PHE cc_start: 0.7778 (m-80) cc_final: 0.7379 (m-80) REVERT: B 27 LEU cc_start: 0.7364 (tt) cc_final: 0.6887 (mp) REVERT: D 27 LEU cc_start: 0.7254 (tt) cc_final: 0.6861 (mp) REVERT: D 34 SER cc_start: 0.8806 (p) cc_final: 0.8554 (m) outliers start: 17 outliers final: 13 residues processed: 55 average time/residue: 0.1101 time to fit residues: 7.7762 Evaluate side-chains 58 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 CYS Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 34 SER 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 E residue 6 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 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN C 22 ASN I 35 ASN K 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2994 Z= 0.207 Angle : 0.608 7.674 4068 Z= 0.314 Chirality : 0.041 0.129 492 Planarity : 0.002 0.009 534 Dihedral : 14.803 59.977 480 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % 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: -4.55 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS H 18 PHE 0.017 0.002 PHE B 23 ARG 0.001 0.000 ARG B 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 fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.312 Fit side-chains REVERT: B 15 PHE cc_start: 0.7580 (m-80) cc_final: 0.7032 (m-80) REVERT: B 27 LEU cc_start: 0.7413 (tt) cc_final: 0.6954 (mp) REVERT: F 15 PHE cc_start: 0.7660 (m-80) cc_final: 0.6213 (p90) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.1025 time to fit residues: 6.6931 Evaluate side-chains 48 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 CYS Chi-restraints excluded: chain A residue 6 THR 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 F residue 32 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.7115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2994 Z= 0.232 Angle : 0.617 8.961 4068 Z= 0.315 Chirality : 0.041 0.130 492 Planarity : 0.002 0.009 534 Dihedral : 14.004 58.794 480 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % 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: -4.51 (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 0.004 0.002 HIS H 18 PHE 0.020 0.002 PHE B 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 53 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.335 Fit side-chains REVERT: B 15 PHE cc_start: 0.7254 (m-80) cc_final: 0.6732 (m-80) REVERT: B 27 LEU cc_start: 0.7415 (tt) cc_final: 0.6972 (mp) REVERT: D 27 LEU cc_start: 0.7255 (tt) cc_final: 0.6831 (mp) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.1053 time to fit residues: 6.6675 Evaluate side-chains 48 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 CYS Chi-restraints excluded: chain A residue 6 THR 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 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 2 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2994 Z= 0.447 Angle : 0.727 8.460 4068 Z= 0.386 Chirality : 0.046 0.146 492 Planarity : 0.003 0.013 534 Dihedral : 16.256 59.635 480 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.70 % Allowed : 18.83 % 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: -4.47 (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 0.008 0.003 HIS J 18 PHE 0.022 0.003 PHE I 15 ARG 0.004 0.001 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 64 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.377 Fit side-chains REVERT: J 34 SER cc_start: 0.8567 (t) cc_final: 0.8326 (p) REVERT: A 27 LEU cc_start: 0.7384 (tt) cc_final: 0.6978 (mp) REVERT: B 15 PHE cc_start: 0.7469 (m-80) cc_final: 0.6981 (m-80) REVERT: B 27 LEU cc_start: 0.7446 (tt) cc_final: 0.6976 (mp) REVERT: D 27 LEU cc_start: 0.7335 (tt) cc_final: 0.6903 (mp) REVERT: F 15 PHE cc_start: 0.7819 (m-80) cc_final: 0.6602 (p90) REVERT: K 11 ARG cc_start: 0.5191 (mmp-170) cc_final: 0.4723 (mmm160) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.1284 time to fit residues: 8.9117 Evaluate side-chains 57 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 34 SER 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 34 SER Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain I residue 10 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.7373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2994 Z= 0.198 Angle : 0.604 9.246 4068 Z= 0.308 Chirality : 0.041 0.128 492 Planarity : 0.002 0.008 534 Dihedral : 13.782 57.109 480 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.47 % Allowed : 21.30 % Favored : 76.23 % 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 : -3.41 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 18 PHE 0.019 0.002 PHE B 23 ARG 0.002 0.000 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 53 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.292 Fit side-chains REVERT: B 15 PHE cc_start: 0.7132 (m-80) cc_final: 0.6690 (m-80) REVERT: B 27 LEU cc_start: 0.7490 (tt) cc_final: 0.7058 (mp) REVERT: D 27 LEU cc_start: 0.7325 (tt) cc_final: 0.6924 (mp) REVERT: K 34 SER cc_start: 0.8512 (t) cc_final: 0.8220 (m) outliers start: 8 outliers final: 8 residues processed: 48 average time/residue: 0.1004 time to fit residues: 6.3225 Evaluate side-chains 49 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 4 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 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2994 Z= 0.361 Angle : 0.678 8.125 4068 Z= 0.358 Chirality : 0.044 0.142 492 Planarity : 0.003 0.011 534 Dihedral : 15.550 59.874 480 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.78 % Allowed : 20.99 % Favored : 76.23 % 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 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 18 PHE 0.019 0.003 PHE B 23 ARG 0.005 0.001 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 53 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.327 Fit side-chains REVERT: B 15 PHE cc_start: 0.7251 (m-80) cc_final: 0.6767 (m-80) REVERT: B 27 LEU cc_start: 0.7496 (tt) cc_final: 0.7053 (mp) REVERT: D 27 LEU cc_start: 0.7320 (tt) cc_final: 0.6920 (mp) REVERT: F 15 PHE cc_start: 0.7761 (m-80) cc_final: 0.6618 (p90) REVERT: K 11 ARG cc_start: 0.5162 (mmp-170) cc_final: 0.4713 (mmm160) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.1126 time to fit residues: 6.8487 Evaluate side-chains 52 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 4 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 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.148054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.117687 restraints weight = 4837.758| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.90 r_work: 0.3764 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.7485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2994 Z= 0.278 Angle : 0.634 7.538 4068 Z= 0.331 Chirality : 0.042 0.131 492 Planarity : 0.002 0.008 534 Dihedral : 15.013 58.672 480 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.47 % Allowed : 20.99 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.28), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.21), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.020 0.002 PHE B 23 ARG 0.004 0.000 ARG F 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1088.54 seconds wall clock time: 19 minutes 52.45 seconds (1192.45 seconds total)