Starting phenix.real_space_refine on Thu Oct 22 21:47:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29hq_57189/10_2026/29hq_57189_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/29hq_57189/10_2026/29hq_57189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/29hq_57189/10_2026/29hq_57189_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29hq_57189/10_2026/29hq_57189_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/29hq_57189/10_2026/29hq_57189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29hq_57189/10_2026/29hq_57189.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 1905 2.51 5 N 575 2.21 5 O 615 1.98 5 H 2910 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6005 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "B" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 351 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 351 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "I" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "J" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "K" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 351 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "M" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "N" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "O" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 351 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "Q" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "R" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "S" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 351 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Time building chain proxies: 1.17, per 1000 atoms: 0.19 Number of scatterers: 6005 At special positions: 0 Unit cell: (78.1, 85.8, 48.4, 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) O 615 8.00 N 575 7.00 C 1905 6.00 H 2910 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.45 Conformation dependent library (CDL) restraints added in 146.4 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 54.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 22 removed outlier: 6.892A pdb=" N ASN A 21 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN E 22 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN E 21 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN I 22 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN I 21 " --> pdb=" O GLY M 20 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN M 22 " --> pdb=" O ASN I 21 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN M 21 " --> pdb=" O GLY Q 20 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN Q 22 " --> pdb=" O ASN M 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.548A pdb=" N SER E 29 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL I 32 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN E 31 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER I 29 " --> pdb=" O THR M 30 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL M 32 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN I 31 " --> pdb=" O VAL M 32 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER M 29 " --> pdb=" O THR Q 30 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL Q 32 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN M 31 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 22 removed outlier: 6.941A pdb=" N ASN B 21 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN F 22 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN F 21 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN J 22 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN J 21 " --> pdb=" O GLY N 20 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN N 22 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN N 21 " --> pdb=" O GLY R 20 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN R 22 " --> pdb=" O ASN N 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.559A pdb=" N SER J 29 " --> pdb=" O THR N 30 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL N 32 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN J 31 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER N 29 " --> pdb=" O THR R 30 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL R 32 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN N 31 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 15 through 18 removed outlier: 6.578A pdb=" N LEU C 16 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN G 14 " --> pdb=" O PHE K 15 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL K 17 " --> pdb=" O ASN G 14 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU G 16 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN K 14 " --> pdb=" O PHE O 15 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL O 17 " --> pdb=" O ASN K 14 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU K 16 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN O 14 " --> pdb=" O PHE S 15 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL S 17 " --> pdb=" O ASN O 14 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU O 16 " --> pdb=" O VAL S 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 27 removed outlier: 6.635A pdb=" N ASN C 22 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ALA G 25 " --> pdb=" O ASN C 22 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY C 24 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU G 27 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 26 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN G 22 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ALA K 25 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY G 24 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU K 27 " --> pdb=" O GLY G 24 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE G 26 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN K 22 " --> pdb=" O PHE O 23 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N ALA O 25 " --> pdb=" O ASN K 22 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY K 24 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU O 27 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE K 26 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN O 22 " --> pdb=" O PHE S 23 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ALA S 25 " --> pdb=" O ASN O 22 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY O 24 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU S 27 " --> pdb=" O GLY O 24 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE O 26 " --> pdb=" O LEU S 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.930A pdb=" N ASN G 31 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL K 32 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL O 32 " --> pdb=" O ASN K 31 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL S 32 " --> pdb=" O ASN O 31 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 36 removed outlier: 6.746A pdb=" N ASN C 35 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN G 35 " --> pdb=" O THR K 36 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN K 35 " --> pdb=" O THR O 36 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN O 35 " --> pdb=" O THR S 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 101 hydrogen bonds defined for protein. 303 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: 1.23 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.07: 765 1.07 - 1.19: 2145 1.19 - 1.31: 554 1.31 - 1.43: 936 1.43 - 1.55: 1650 Bond restraints: 6050 Sorted by residual: bond pdb=" N ASN O 22 " pdb=" H ASN O 22 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE M 26 " pdb=" H ILE M 26 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN C 21 " pdb="HD22 ASN C 21 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 PHE K 23 " pdb=" HE1 PHE K 23 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 TYR F 37 " pdb=" HE1 TYR F 37 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 7564 1.70 - 3.40: 2069 3.40 - 5.10: 637 5.10 - 6.80: 406 6.80 - 8.49: 14 Bond angle restraints: 10690 Sorted by residual: angle pdb=" CB HIS Q 18 " pdb=" CG HIS Q 18 " pdb=" CD2 HIS Q 18 " ideal model delta sigma weight residual 131.20 124.92 6.28 1.30e+00 5.92e-01 2.33e+01 angle pdb=" CA ASN B 21 " pdb=" CB ASN B 21 " pdb=" CG ASN B 21 " ideal model delta sigma weight residual 112.60 117.43 -4.83 1.00e+00 1.00e+00 2.33e+01 angle pdb=" CA ASN J 21 " pdb=" CB ASN J 21 " pdb=" CG ASN J 21 " ideal model delta sigma weight residual 112.60 117.41 -4.81 1.00e+00 1.00e+00 2.31e+01 angle pdb=" CA ASN N 21 " pdb=" CB ASN N 21 " pdb=" CG ASN N 21 " ideal model delta sigma weight residual 112.60 117.39 -4.79 1.00e+00 1.00e+00 2.30e+01 angle pdb=" CA ASN E 21 " pdb=" CB ASN E 21 " pdb=" CG ASN E 21 " ideal model delta sigma weight residual 112.60 117.31 -4.71 1.00e+00 1.00e+00 2.22e+01 ... (remaining 10685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.46: 2603 13.46 - 26.92: 169 26.92 - 40.38: 40 40.38 - 53.84: 31 53.84 - 67.30: 57 Dihedral angle restraints: 2900 sinusoidal: 1490 harmonic: 1410 Sorted by residual: dihedral pdb=" CA LEU J 12 " pdb=" C LEU J 12 " pdb=" N ALA J 13 " pdb=" CA ALA J 13 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU C 27 " pdb=" C LEU C 27 " pdb=" N SER C 28 " pdb=" CA SER C 28 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LEU B 12 " pdb=" C LEU B 12 " pdb=" N ALA B 13 " pdb=" CA ALA B 13 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 2897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 256 0.054 - 0.108: 154 0.108 - 0.162: 59 0.162 - 0.216: 22 0.216 - 0.270: 4 Chirality restraints: 495 Sorted by residual: chirality pdb=" CA SER B 34 " pdb=" N SER B 34 " pdb=" C SER B 34 " pdb=" CB SER B 34 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA SER R 34 " pdb=" N SER R 34 " pdb=" C SER R 34 " pdb=" CB SER R 34 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA SER J 34 " pdb=" N SER J 34 " pdb=" C SER J 34 " pdb=" CB SER J 34 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 492 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 37 " 0.100 2.00e-02 2.50e+03 4.21e-02 5.32e+01 pdb=" CG TYR O 37 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR O 37 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR O 37 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR O 37 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR O 37 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR O 37 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR O 37 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 TYR O 37 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR O 37 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR O 37 " -0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR O 37 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 15 " -0.107 2.00e-02 2.50e+03 4.02e-02 4.84e+01 pdb=" CG PHE G 15 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE G 15 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE G 15 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE G 15 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE G 15 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE G 15 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE G 15 " 0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE G 15 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 PHE G 15 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE G 15 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE G 15 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 15 " -0.084 2.00e-02 2.50e+03 3.84e-02 4.42e+01 pdb=" CG PHE O 15 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE O 15 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE O 15 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE O 15 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE O 15 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE O 15 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE O 15 " 0.080 2.00e-02 2.50e+03 pdb=" HD2 PHE O 15 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 PHE O 15 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 PHE O 15 " 0.024 2.00e-02 2.50e+03 pdb=" HZ PHE O 15 " -0.033 2.00e-02 2.50e+03 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.25: 800 2.25 - 2.81: 10516 2.81 - 3.38: 13905 3.38 - 3.94: 20917 3.94 - 4.50: 27567 Nonbonded interactions: 73705 Sorted by model distance: nonbonded pdb=" O ILE E 26 " pdb=" HG SER E 28 " model vdw 1.690 2.450 nonbonded pdb=" O ILE J 26 " pdb=" HG SER J 28 " model vdw 1.707 2.450 nonbonded pdb=" O ILE I 26 " pdb=" HG SER I 28 " model vdw 1.710 2.450 nonbonded pdb=" HB3 LEU E 12 " pdb="HD22 ASN K 14 " model vdw 1.717 2.270 nonbonded pdb=" O ILE A 26 " pdb=" HG SER A 28 " model vdw 1.732 2.450 ... (remaining 73700 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' and resid 13 through 38) selection = (chain 'B' and resid 13 through 38) selection = chain 'C' selection = (chain 'E' and resid 13 through 38) selection = (chain 'F' and resid 13 through 38) selection = chain 'G' selection = (chain 'I' and resid 13 through 38) selection = (chain 'J' and resid 13 through 38) selection = chain 'K' selection = (chain 'M' and resid 13 through 38) selection = (chain 'N' and resid 13 through 38) selection = chain 'O' selection = (chain 'Q' and resid 13 through 38) selection = (chain 'R' and resid 13 through 38) selection = chain 'S' } 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 group one per residue 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.240 Find NCS groups from input model: 0.100 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.1657 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 : 0.011 0.033 3140 Z= 0.698 Angle : 1.827 7.070 4265 Z= 1.245 Chirality : 0.080 0.270 495 Planarity : 0.010 0.050 570 Dihedral : 11.864 64.755 1005 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.30), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.23), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG E 11 TYR 0.094 0.019 TYR O 37 PHE 0.069 0.012 PHE G 15 HIS 0.031 0.008 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.01110 / 0.70 ( 3140) covalent geometry : angle 1.82708 / 1.24 ( 4265) hydrogen bonds : bond 0.12230 / 8.37 ( 101) hydrogen bonds : angle 6.92052 / 4.73 ( 303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0594 time to fit residues: 2.2878 Evaluate side-chains 10 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 ASN B 21 ASN C 14 ASN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 21 ASN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN N 21 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN Q 35 ASN R 21 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.145330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.128450 restraints weight = 12570.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.133162 restraints weight = 4751.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.136177 restraints weight = 2460.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.138213 restraints weight = 1529.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.139585 restraints weight = 1060.693| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0197 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3140 Z= 0.214 Angle : 0.660 3.484 4265 Z= 0.378 Chirality : 0.049 0.171 495 Planarity : 0.004 0.013 570 Dihedral : 5.879 19.373 425 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.76 % Allowed : 0.88 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.25), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.19), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 11 TYR 0.012 0.002 TYR N 37 PHE 0.010 0.002 PHE J 23 HIS 0.007 0.002 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 ( 3140) covalent geometry : angle 0.65972 / 0.38 ( 4265) hydrogen bonds : bond 0.03317 / 2.40 ( 101) hydrogen bonds : angle 5.32691 / 3.80 ( 303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.162 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 17 average time/residue: 0.0573 time to fit residues: 1.6196 Evaluate side-chains 11 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain J residue 14 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [39, 8, 1, 38, 25, 27, 22, 19, 9, 18, 31] chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.151716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.133622 restraints weight = 11810.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.138720 restraints weight = 4836.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.142140 restraints weight = 2542.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.144432 restraints weight = 1569.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.145881 restraints weight = 1066.379| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0204 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3140 Z= 0.122 Angle : 0.449 2.771 4265 Z= 0.263 Chirality : 0.046 0.148 495 Planarity : 0.002 0.015 570 Dihedral : 4.508 14.488 425 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.88 % Allowed : 1.76 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.26), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.20), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 11 TYR 0.005 0.001 TYR J 37 PHE 0.015 0.001 PHE K 15 HIS 0.002 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 3140) covalent geometry : angle 0.44883 / 0.26 ( 4265) hydrogen bonds : bond 0.02823 / 1.95 ( 101) hydrogen bonds : angle 4.73857 / 3.38 ( 303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.142 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 14 average time/residue: 0.0614 time to fit residues: 1.4560 Evaluate side-chains 12 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain J residue 14 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [39, 35, 28, 8, 24, 30, 19, 31, 13, 27, 20] chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 ASN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN M 18 HIS N 35 ASN Q 18 HIS ** S 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.215454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.188457 restraints weight = 9444.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.196935 restraints weight = 4399.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.202494 restraints weight = 2436.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.205977 restraints weight = 1494.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.208649 restraints weight = 1012.391| |-----------------------------------------------------------------------------| r_work (final): 0.4813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2250 moved from start: 1.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3140 Z= 0.232 Angle : 0.696 7.207 4265 Z= 0.394 Chirality : 0.054 0.254 495 Planarity : 0.004 0.031 570 Dihedral : 5.234 23.296 425 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.88 % Allowed : 4.41 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.26), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 11 TYR 0.012 0.002 TYR J 37 PHE 0.039 0.004 PHE O 15 HIS 0.006 0.001 HIS K 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.23 ( 3140) covalent geometry : angle 0.69622 / 0.39 ( 4265) hydrogen bonds : bond 0.04105 / 2.99 ( 101) hydrogen bonds : angle 5.35475 / 3.79 ( 303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: E 23 PHE cc_start: 0.4743 (m-80) cc_final: 0.4042 (m-80) outliers start: 3 outliers final: 2 residues processed: 29 average time/residue: 0.0593 time to fit residues: 2.6138 Evaluate side-chains 22 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain J residue 14 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [11, 12, 1, 21, 36, 29, 22, 4, 30, 23, 2] chunk 11 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 14 ASN S 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.226318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.191871 restraints weight = 9820.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.200457 restraints weight = 4805.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.205872 restraints weight = 2976.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.209311 restraints weight = 2095.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.212025 restraints weight = 1620.746| |-----------------------------------------------------------------------------| r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3925 moved from start: 1.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 3140 Z= 0.349 Angle : 0.762 5.607 4265 Z= 0.434 Chirality : 0.053 0.199 495 Planarity : 0.004 0.034 570 Dihedral : 5.842 19.831 425 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.06 % Allowed : 7.06 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.27), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.21), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG A 11 TYR 0.017 0.003 TYR R 37 PHE 0.036 0.005 PHE I 23 HIS 0.010 0.003 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.35 ( 3140) covalent geometry : angle 0.76216 / 0.43 ( 4265) hydrogen bonds : bond 0.04679 / 3.18 ( 101) hydrogen bonds : angle 5.52661 / 3.87 ( 303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.6638 (t0) cc_final: 0.6217 (t0) REVERT: G 23 PHE cc_start: 0.3865 (OUTLIER) cc_final: 0.3654 (t80) REVERT: G 35 ASN cc_start: 0.6935 (m-40) cc_final: 0.6686 (m-40) REVERT: K 35 ASN cc_start: 0.6137 (m-40) cc_final: 0.5785 (m-40) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 0.0581 time to fit residues: 4.5204 Evaluate side-chains 46 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain G residue 23 PHE Chi-restraints excluded: chain R residue 12 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [30, 9, 35, 22, 32, 23, 17, 20, 34, 27, 15] chunk 30 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN ** S 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.218939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.185635 restraints weight = 9646.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.193299 restraints weight = 4770.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.198639 restraints weight = 2965.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.202302 restraints weight = 2089.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.204901 restraints weight = 1597.414| |-----------------------------------------------------------------------------| r_work (final): 0.4906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4217 moved from start: 1.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3140 Z= 0.132 Angle : 0.500 3.510 4265 Z= 0.288 Chirality : 0.045 0.146 495 Planarity : 0.002 0.012 570 Dihedral : 4.702 18.285 425 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.76 % Allowed : 10.59 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.25), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.19), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 11 TYR 0.012 0.002 TYR M 37 PHE 0.011 0.002 PHE Q 23 HIS 0.006 0.001 HIS G 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 3140) covalent geometry : angle 0.50043 / 0.29 ( 4265) hydrogen bonds : bond 0.02736 / 1.87 ( 101) hydrogen bonds : angle 4.68702 / 3.26 ( 303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.3546 (m-80) cc_final: 0.3292 (m-80) REVERT: G 23 PHE cc_start: 0.4629 (m-80) cc_final: 0.4420 (t80) REVERT: K 35 ASN cc_start: 0.6802 (m-40) cc_final: 0.6538 (m110) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.0643 time to fit residues: 4.2854 Evaluate side-chains 45 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain I residue 12 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [7, 1, 21, 17, 25, 33, 15, 30, 14, 24, 34] chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.206449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.176515 restraints weight = 9859.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.183564 restraints weight = 4419.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.188309 restraints weight = 2626.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.191497 restraints weight = 1821.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.193701 restraints weight = 1393.351| |-----------------------------------------------------------------------------| r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5330 moved from start: 1.9662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 3140 Z= 0.232 Angle : 0.691 7.964 4265 Z= 0.394 Chirality : 0.052 0.317 495 Planarity : 0.004 0.024 570 Dihedral : 5.784 24.641 425 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.18 % Allowed : 12.06 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.10 (0.25), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.19), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 11 TYR 0.011 0.002 TYR A 37 PHE 0.034 0.003 PHE I 23 HIS 0.014 0.002 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 ( 3140) covalent geometry : angle 0.69101 / 0.39 ( 4265) hydrogen bonds : bond 0.03364 / 2.28 ( 101) hydrogen bonds : angle 4.81930 / 3.25 ( 303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.7243 (m-80) cc_final: 0.5936 (p90) REVERT: C 35 ASN cc_start: 0.9164 (m-40) cc_final: 0.8961 (m-40) REVERT: I 31 ASN cc_start: 0.6835 (m-40) cc_final: 0.6432 (m-40) REVERT: J 32 VAL cc_start: 0.7982 (t) cc_final: 0.7699 (t) outliers start: 4 outliers final: 2 residues processed: 67 average time/residue: 0.0851 time to fit residues: 7.6711 Evaluate side-chains 58 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 23 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [23, 3, 4, 24, 11, 13, 35, 32, 30, 20, 26] chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.195650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.166648 restraints weight = 10155.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.173541 restraints weight = 4364.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.178161 restraints weight = 2564.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.181289 restraints weight = 1780.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.183316 restraints weight = 1355.639| |-----------------------------------------------------------------------------| r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 2.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3140 Z= 0.161 Angle : 0.577 6.604 4265 Z= 0.318 Chirality : 0.045 0.152 495 Planarity : 0.003 0.051 570 Dihedral : 5.241 21.203 425 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.47 % Allowed : 13.24 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.24), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.18), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 11 TYR 0.014 0.002 TYR E 37 PHE 0.013 0.002 PHE Q 23 HIS 0.008 0.002 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 3140) covalent geometry : angle 0.57726 / 0.32 ( 4265) hydrogen bonds : bond 0.02413 / 1.58 ( 101) hydrogen bonds : angle 4.56967 / 3.10 ( 303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ILE cc_start: 0.6666 (mt) cc_final: 0.6442 (mt) REVERT: E 18 HIS cc_start: 0.7304 (m-70) cc_final: 0.7070 (t-90) REVERT: E 37 TYR cc_start: 0.8204 (m-80) cc_final: 0.7683 (m-80) REVERT: I 31 ASN cc_start: 0.7466 (m-40) cc_final: 0.6839 (m-40) REVERT: R 32 VAL cc_start: 0.7542 (t) cc_final: 0.7154 (t) outliers start: 5 outliers final: 1 residues processed: 64 average time/residue: 0.0641 time to fit residues: 5.8709 Evaluate side-chains 58 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [28, 21, 19, 11, 8, 25, 13, 30, 27, 9, 36] chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN N 35 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.183952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.157603 restraints weight = 10689.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.163630 restraints weight = 4583.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.167618 restraints weight = 2737.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.170254 restraints weight = 1932.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.172096 restraints weight = 1508.651| |-----------------------------------------------------------------------------| r_work (final): 0.4773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 2.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3140 Z= 0.173 Angle : 0.627 6.915 4265 Z= 0.346 Chirality : 0.048 0.191 495 Planarity : 0.003 0.023 570 Dihedral : 5.367 24.643 425 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 1.18 % Allowed : 16.18 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.26), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.20), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 11 TYR 0.014 0.002 TYR B 37 PHE 0.024 0.003 PHE G 23 HIS 0.018 0.003 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 3140) covalent geometry : angle 0.62704 / 0.35 ( 4265) hydrogen bonds : bond 0.02743 / 1.78 ( 101) hydrogen bonds : angle 4.45378 / 3.02 ( 303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.6852 (mtt-85) cc_final: 0.5897 (mmt180) REVERT: E 31 ASN cc_start: 0.7723 (m-40) cc_final: 0.7286 (m-40) REVERT: I 31 ASN cc_start: 0.8069 (m-40) cc_final: 0.7566 (m-40) REVERT: I 35 ASN cc_start: 0.9133 (m-40) cc_final: 0.8697 (m-40) REVERT: K 35 ASN cc_start: 0.9086 (m-40) cc_final: 0.8880 (m-40) REVERT: M 37 TYR cc_start: 0.7263 (m-80) cc_final: 0.6183 (m-80) REVERT: R 32 VAL cc_start: 0.8178 (t) cc_final: 0.7769 (t) REVERT: S 35 ASN cc_start: 0.7659 (m-40) cc_final: 0.6345 (p0) outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.0923 time to fit residues: 10.2246 Evaluate side-chains 76 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain M residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [39, 27, 1, 38, 18, 13, 7, 35, 3, 10, 8] chunk 39 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 GLN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.183731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.157042 restraints weight = 10659.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.163308 restraints weight = 4400.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.167377 restraints weight = 2576.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.170125 restraints weight = 1806.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.171907 restraints weight = 1396.447| |-----------------------------------------------------------------------------| r_work (final): 0.4805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 2.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3140 Z= 0.092 Angle : 0.510 7.367 4265 Z= 0.271 Chirality : 0.045 0.142 495 Planarity : 0.002 0.009 570 Dihedral : 4.802 19.014 425 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 18.82 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.27), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.20), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 11 TYR 0.005 0.001 TYR G 37 PHE 0.018 0.001 PHE I 23 HIS 0.005 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 ( 3140) covalent geometry : angle 0.50996 / 0.27 ( 4265) hydrogen bonds : bond 0.01892 / 1.22 ( 101) hydrogen bonds : angle 4.17594 / 2.84 ( 303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.6683 (mtt-85) cc_final: 0.5832 (mmt180) REVERT: E 22 ASN cc_start: 0.8692 (t0) cc_final: 0.8295 (t0) REVERT: E 31 ASN cc_start: 0.7756 (m-40) cc_final: 0.7450 (m-40) REVERT: I 31 ASN cc_start: 0.8075 (m-40) cc_final: 0.7547 (m-40) REVERT: I 35 ASN cc_start: 0.8960 (m-40) cc_final: 0.8639 (m110) REVERT: M 37 TYR cc_start: 0.7405 (m-80) cc_final: 0.6493 (m-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0803 time to fit residues: 8.2635 Evaluate side-chains 71 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: [36, 24, 2, 30, 33, 8, 12, 15, 13, 25, 3] chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN I 10 GLN I 21 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.152487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.130183 restraints weight = 12053.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.135107 restraints weight = 4793.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.138238 restraints weight = 2786.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.140313 restraints weight = 1973.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.141434 restraints weight = 1555.989| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 2.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3140 Z= 0.292 Angle : 0.858 6.153 4265 Z= 0.484 Chirality : 0.054 0.182 495 Planarity : 0.005 0.063 570 Dihedral : 6.933 30.570 425 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 0.59 % Allowed : 19.12 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.26), residues: 385 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.20), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 11 TYR 0.019 0.004 TYR C 37 PHE 0.037 0.005 PHE G 23 HIS 0.009 0.003 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.29 ( 3140) covalent geometry : angle 0.85759 / 0.48 ( 4265) hydrogen bonds : bond 0.03973 / 2.58 ( 101) hydrogen bonds : angle 5.51951 / 3.70 ( 303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.17 seconds wall clock time: 27 minutes 25.69 seconds (1645.69 seconds total)