Starting phenix.real_space_refine on Wed Feb 14 03:42:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eht_28152/02_2024/8eht_28152.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eht_28152/02_2024/8eht_28152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eht_28152/02_2024/8eht_28152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eht_28152/02_2024/8eht_28152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eht_28152/02_2024/8eht_28152.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eht_28152/02_2024/8eht_28152.pdb" } resolution = 3.4 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= 0.009 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 14 5.16 5 C 5222 2.51 5 N 1470 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 29": "OD1" <-> "OD2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "F ASP 6": "OD1" <-> "OD2" Residue "F PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 63": "OD1" <-> "OD2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ASP 115": "OD1" <-> "OD2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 152": "OD1" <-> "OD2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D ASP 152": "OD1" <-> "OD2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E ASP 119": "OD1" <-> "OD2" Residue "E ASP 159": "OD1" <-> "OD2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W ASP 63": "OD1" <-> "OD2" Residue "W ASP 68": "OD1" <-> "OD2" Residue "W TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 75": "OD1" <-> "OD2" Residue "W ASP 115": "OD1" <-> "OD2" Residue "W GLU 130": "OE1" <-> "OE2" Residue "W ASP 159": "OD1" <-> "OD2" Residue "W ASP 170": "OD1" <-> "OD2" Residue "X ASP 6": "OD1" <-> "OD2" Residue "X PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "X TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 63": "OD1" <-> "OD2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8554 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1222 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "F" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1222 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "D" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1222 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "E" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1222 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "W" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1222 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "X" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1222 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1222 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Time building chain proxies: 5.21, per 1000 atoms: 0.61 Number of scatterers: 8554 At special positions: 0 Unit cell: (97.02, 93.786, 120.736, 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 14 16.00 O 1848 8.00 N 1470 7.00 C 5222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 62 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 62 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 62 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 62 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.42 Conformation dependent library (CDL) restraints added in 1.8 seconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 19 sheets defined 5.9% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'C' and resid 40 through 47 Processing helix chain 'F' and resid 40 through 47 Processing helix chain 'D' and resid 27 through 29 No H-bonds generated for 'chain 'D' and resid 27 through 29' Processing helix chain 'D' and resid 40 through 47 Processing helix chain 'E' and resid 27 through 29 No H-bonds generated for 'chain 'E' and resid 27 through 29' Processing helix chain 'E' and resid 40 through 47 Processing helix chain 'W' and resid 27 through 29 No H-bonds generated for 'chain 'W' and resid 27 through 29' Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'X' and resid 27 through 29 No H-bonds generated for 'chain 'X' and resid 27 through 29' Processing helix chain 'X' and resid 40 through 47 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 40 through 47 Processing sheet with id=AA1, first strand: chain 'F' and resid 31 through 35 removed outlier: 8.454A pdb=" N LYS F 32 " --> pdb=" O GLN C 9 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR C 11 " --> pdb=" O LYS F 32 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE F 34 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN C 13 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER C 8 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA F 160 " --> pdb=" O PHE C 14 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F 158 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE F 69 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR F 71 " --> pdb=" O GLN F 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 25 Processing sheet with id=AA3, first strand: chain 'C' and resid 116 through 118 removed outlier: 4.013A pdb=" N ILE C 69 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 31 through 35 removed outlier: 8.409A pdb=" N LYS D 32 " --> pdb=" O GLN F 9 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR F 11 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE D 34 " --> pdb=" O THR F 11 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASN F 13 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER F 8 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE D 69 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 17 through 18 Processing sheet with id=AA6, first strand: chain 'F' and resid 24 through 25 Processing sheet with id=AA7, first strand: chain 'E' and resid 31 through 39 removed outlier: 8.556A pdb=" N LYS E 32 " --> pdb=" O GLN D 9 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR D 11 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE E 34 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN D 13 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU E 36 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N SER D 15 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU E 38 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG D 17 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE E 69 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 25 Processing sheet with id=AA9, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.695A pdb=" N ASN D 126 " --> pdb=" O ASN D 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 31 through 39 removed outlier: 8.529A pdb=" N LYS W 32 " --> pdb=" O GLN E 9 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR E 11 " --> pdb=" O LYS W 32 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE W 34 " --> pdb=" O THR E 11 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASN E 13 " --> pdb=" O ILE W 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU W 36 " --> pdb=" O ASN E 13 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER E 15 " --> pdb=" O LEU W 36 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU W 38 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG E 17 " --> pdb=" O GLU W 38 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER E 8 " --> pdb=" O ILE W 166 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE W 69 " --> pdb=" O LEU W 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 24 through 25 Processing sheet with id=AB3, first strand: chain 'X' and resid 31 through 38 removed outlier: 8.431A pdb=" N LYS X 32 " --> pdb=" O GLN W 9 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR W 11 " --> pdb=" O LYS X 32 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE X 34 " --> pdb=" O THR W 11 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASN W 13 " --> pdb=" O ILE X 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU X 36 " --> pdb=" O ASN W 13 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER W 15 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU X 38 " --> pdb=" O SER W 15 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG W 17 " --> pdb=" O GLU X 38 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER W 8 " --> pdb=" O ILE X 166 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE X 69 " --> pdb=" O LEU X 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 24 through 25 Processing sheet with id=AB5, first strand: chain 'W' and resid 122 through 123 removed outlier: 3.500A pdb=" N ASN W 126 " --> pdb=" O ASN W 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 31 through 35 removed outlier: 8.521A pdb=" N LYS B 32 " --> pdb=" O GLN X 9 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR X 11 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 34 " --> pdb=" O THR X 11 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN X 13 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER X 8 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 158 " --> pdb=" O GLY X 16 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE B 69 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 24 through 25 Processing sheet with id=AB8, first strand: chain 'X' and resid 122 through 123 removed outlier: 3.570A pdb=" N ASN X 126 " --> pdb=" O ASN X 123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 24 through 25 Processing sheet with id=AC1, first strand: chain 'B' and resid 122 through 123 281 hydrogen bonds defined for protein. 714 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: 2.07 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2975 1.34 - 1.45: 807 1.45 - 1.57: 4828 1.57 - 1.69: 0 1.69 - 1.80: 14 Bond restraints: 8624 Sorted by residual: bond pdb=" N ALA X 1 " pdb=" CA ALA X 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" N ALA E 1 " pdb=" CA ALA E 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.63e+00 bond pdb=" N ALA B 1 " pdb=" CA ALA B 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.57e+00 bond pdb=" N ALA D 1 " pdb=" CA ALA D 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.48e+00 bond pdb=" N ALA F 1 " pdb=" CA ALA F 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.43e+00 ... (remaining 8619 not shown) Histogram of bond angle deviations from ideal: 102.34 - 107.73: 194 107.73 - 113.12: 5046 113.12 - 118.50: 1837 118.50 - 123.89: 4627 123.89 - 129.28: 70 Bond angle restraints: 11774 Sorted by residual: angle pdb=" N THR E 151 " pdb=" CA THR E 151 " pdb=" C THR E 151 " ideal model delta sigma weight residual 111.28 115.36 -4.08 1.09e+00 8.42e-01 1.40e+01 angle pdb=" N THR F 151 " pdb=" CA THR F 151 " pdb=" C THR F 151 " ideal model delta sigma weight residual 111.28 115.18 -3.90 1.09e+00 8.42e-01 1.28e+01 angle pdb=" N THR X 151 " pdb=" CA THR X 151 " pdb=" C THR X 151 " ideal model delta sigma weight residual 111.28 115.12 -3.84 1.09e+00 8.42e-01 1.24e+01 angle pdb=" N THR D 151 " pdb=" CA THR D 151 " pdb=" C THR D 151 " ideal model delta sigma weight residual 111.28 115.10 -3.82 1.09e+00 8.42e-01 1.23e+01 angle pdb=" N THR W 151 " pdb=" CA THR W 151 " pdb=" C THR W 151 " ideal model delta sigma weight residual 111.28 114.44 -3.16 1.09e+00 8.42e-01 8.39e+00 ... (remaining 11769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4868 18.00 - 36.00: 297 36.00 - 54.00: 72 54.00 - 72.00: 1 72.00 - 90.00: 5 Dihedral angle restraints: 5243 sinusoidal: 1827 harmonic: 3416 Sorted by residual: dihedral pdb=" CA GLN F 24 " pdb=" C GLN F 24 " pdb=" N VAL F 25 " pdb=" CA VAL F 25 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CB CYS X 23 " pdb=" SG CYS X 23 " pdb=" SG CYS X 62 " pdb=" CB CYS X 62 " ideal model delta sinusoidal sigma weight residual 93.00 126.66 -33.66 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CA GLN W 24 " pdb=" C GLN W 24 " pdb=" N VAL W 25 " pdb=" CA VAL W 25 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 807 0.033 - 0.066: 478 0.066 - 0.098: 83 0.098 - 0.131: 119 0.131 - 0.164: 18 Chirality restraints: 1505 Sorted by residual: chirality pdb=" CA THR D 151 " pdb=" N THR D 151 " pdb=" C THR D 151 " pdb=" CB THR D 151 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA ILE D 133 " pdb=" N ILE D 133 " pdb=" C ILE D 133 " pdb=" CB ILE D 133 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA THR F 151 " pdb=" N THR F 151 " pdb=" C THR F 151 " pdb=" CB THR F 151 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 1502 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE X 149 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C ILE X 149 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE X 149 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY X 150 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 108 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO F 109 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 109 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 109 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 87 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO F 88 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.015 5.00e-02 4.00e+02 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 46 2.59 - 3.16: 6892 3.16 - 3.74: 11280 3.74 - 4.32: 16671 4.32 - 4.90: 29850 Nonbonded interactions: 64739 Sorted by model distance: nonbonded pdb=" OG1 THR F 96 " pdb=" OG1 THR F 154 " model vdw 2.007 2.440 nonbonded pdb=" O ALA F 171 " pdb=" OG1 THR F 172 " model vdw 2.141 2.440 nonbonded pdb=" NZ LYS D 26 " pdb=" OD1 ASP D 28 " model vdw 2.167 2.520 nonbonded pdb=" O ALA E 171 " pdb=" OG1 THR E 172 " model vdw 2.193 2.440 nonbonded pdb=" O ALA D 171 " pdb=" OG1 THR D 172 " model vdw 2.212 2.440 ... (remaining 64734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'W' selection = chain 'X' } 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: 0.530 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: 0.000 Extract box with map and model: 2.410 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.590 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.006 0.042 8624 Z= 0.413 Angle : 0.635 5.058 11774 Z= 0.380 Chirality : 0.050 0.164 1505 Planarity : 0.003 0.042 1554 Dihedral : 12.606 89.995 3024 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.21 % Allowed : 0.64 % Favored : 99.15 % 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: -1.03 (0.22), residues: 1190 helix: -2.03 (0.63), residues: 56 sheet: -0.23 (0.32), residues: 210 loop : -0.73 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE D 55 TYR 0.012 0.002 TYR E 138 ARG 0.005 0.001 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 82 THR cc_start: 0.8046 (m) cc_final: 0.7674 (t) REVERT: F 56 GLN cc_start: 0.7976 (mt0) cc_final: 0.7739 (mt0) REVERT: F 119 ASP cc_start: 0.8129 (m-30) cc_final: 0.7748 (m-30) REVERT: D 144 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7627 (mtp180) REVERT: E 124 LYS cc_start: 0.8336 (mmtp) cc_final: 0.8021 (mtmt) REVERT: E 159 ASP cc_start: 0.7789 (m-30) cc_final: 0.7540 (m-30) REVERT: X 75 ASP cc_start: 0.8180 (t0) cc_final: 0.7970 (t0) REVERT: X 115 ASP cc_start: 0.7897 (p0) cc_final: 0.7646 (p0) outliers start: 2 outliers final: 1 residues processed: 208 average time/residue: 0.1912 time to fit residues: 55.6187 Evaluate side-chains 129 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 152 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN F 53 GLN D 53 GLN D 142 GLN E 13 ASN W 9 GLN B 9 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8624 Z= 0.373 Angle : 0.575 6.541 11774 Z= 0.310 Chirality : 0.048 0.157 1505 Planarity : 0.004 0.028 1554 Dihedral : 5.782 48.335 1255 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.56 % Allowed : 6.29 % Favored : 91.15 % 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: -0.29 (0.23), residues: 1190 helix: -1.00 (0.71), residues: 56 sheet: 0.35 (0.27), residues: 322 loop : -0.32 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE F 101 TYR 0.012 0.002 TYR W 138 ARG 0.004 0.001 ARG X 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 GLN cc_start: 0.7980 (mt0) cc_final: 0.7687 (mt0) REVERT: D 144 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7634 (mtp180) REVERT: E 42 SER cc_start: 0.8746 (m) cc_final: 0.8534 (p) REVERT: W 70 SER cc_start: 0.8915 (p) cc_final: 0.8461 (m) outliers start: 24 outliers final: 20 residues processed: 135 average time/residue: 0.1981 time to fit residues: 37.3400 Evaluate side-chains 124 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain W residue 9 GLN Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 0.0060 chunk 108 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 GLN W 9 GLN B 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8624 Z= 0.169 Angle : 0.453 5.330 11774 Z= 0.244 Chirality : 0.045 0.144 1505 Planarity : 0.003 0.025 1554 Dihedral : 5.092 40.982 1255 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.81 % Allowed : 8.32 % Favored : 89.87 % 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: 0.06 (0.22), residues: 1190 helix: -0.73 (0.72), residues: 56 sheet: 1.09 (0.27), residues: 308 loop : -0.30 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE E 55 TYR 0.009 0.001 TYR W 71 ARG 0.002 0.000 ARG D 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 GLN cc_start: 0.7743 (mt0) cc_final: 0.7536 (mt0) REVERT: F 132 VAL cc_start: 0.9106 (p) cc_final: 0.8895 (t) REVERT: D 118 LEU cc_start: 0.8679 (tp) cc_final: 0.8471 (tp) REVERT: D 144 ARG cc_start: 0.7947 (mtp180) cc_final: 0.7655 (mtt180) REVERT: W 70 SER cc_start: 0.8837 (p) cc_final: 0.8494 (m) REVERT: W 103 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7880 (mt-10) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 0.2170 time to fit residues: 37.0940 Evaluate side-chains 118 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8624 Z= 0.330 Angle : 0.520 5.770 11774 Z= 0.279 Chirality : 0.047 0.150 1505 Planarity : 0.003 0.027 1554 Dihedral : 5.431 47.140 1255 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.77 % Allowed : 9.38 % Favored : 87.85 % 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: 0.02 (0.22), residues: 1190 helix: -0.51 (0.73), residues: 56 sheet: 0.97 (0.27), residues: 322 loop : -0.33 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE E 55 TYR 0.010 0.002 TYR W 71 ARG 0.003 0.001 ARG X 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 GLN cc_start: 0.7743 (mt0) cc_final: 0.7525 (mt0) REVERT: F 132 VAL cc_start: 0.9160 (p) cc_final: 0.8909 (t) REVERT: D 49 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8399 (mtmm) REVERT: D 144 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7671 (mtt180) REVERT: W 70 SER cc_start: 0.8979 (p) cc_final: 0.8489 (m) REVERT: W 103 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7830 (mt-10) outliers start: 26 outliers final: 21 residues processed: 125 average time/residue: 0.2070 time to fit residues: 35.3363 Evaluate side-chains 123 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 0.0670 chunk 38 optimal weight: 9.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8624 Z= 0.280 Angle : 0.486 5.370 11774 Z= 0.261 Chirality : 0.046 0.147 1505 Planarity : 0.003 0.026 1554 Dihedral : 5.290 45.886 1255 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.99 % Allowed : 11.19 % Favored : 85.82 % 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: -0.23 (0.22), residues: 1190 helix: -0.48 (0.73), residues: 56 sheet: 1.16 (0.31), residues: 224 loop : -0.49 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE E 55 TYR 0.010 0.002 TYR W 71 ARG 0.002 0.001 ARG D 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 GLN cc_start: 0.7669 (mt0) cc_final: 0.7468 (mt0) REVERT: F 132 VAL cc_start: 0.9151 (p) cc_final: 0.8908 (t) REVERT: D 144 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7657 (mtt180) REVERT: W 70 SER cc_start: 0.8906 (p) cc_final: 0.8474 (m) REVERT: W 103 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7824 (mt-10) REVERT: W 131 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: X 9 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8260 (mm-40) outliers start: 28 outliers final: 24 residues processed: 117 average time/residue: 0.2233 time to fit residues: 35.6845 Evaluate side-chains 121 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 142 GLN D 142 GLN W 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8624 Z= 0.316 Angle : 0.504 5.414 11774 Z= 0.270 Chirality : 0.046 0.148 1505 Planarity : 0.003 0.027 1554 Dihedral : 5.390 48.575 1255 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.09 % Allowed : 11.30 % Favored : 85.61 % 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: -0.02 (0.22), residues: 1190 helix: -0.44 (0.74), residues: 56 sheet: 1.04 (0.26), residues: 322 loop : -0.42 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE E 55 TYR 0.010 0.002 TYR W 71 ARG 0.003 0.001 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 GLN cc_start: 0.7697 (mt0) cc_final: 0.7484 (mt0) REVERT: D 144 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7711 (mtt180) REVERT: E 116 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.6833 (mp10) REVERT: W 70 SER cc_start: 0.8943 (p) cc_final: 0.8470 (m) REVERT: W 103 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7794 (mt-10) REVERT: W 131 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: X 9 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8233 (mm-40) outliers start: 29 outliers final: 25 residues processed: 114 average time/residue: 0.2390 time to fit residues: 36.3855 Evaluate side-chains 114 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 GLN W 9 GLN ** X 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8624 Z= 0.245 Angle : 0.469 5.083 11774 Z= 0.250 Chirality : 0.045 0.146 1505 Planarity : 0.003 0.026 1554 Dihedral : 5.163 46.516 1255 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.09 % Allowed : 11.73 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.22), residues: 1190 helix: -0.42 (0.74), residues: 56 sheet: 1.23 (0.31), residues: 224 loop : -0.46 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE E 55 TYR 0.010 0.002 TYR W 71 ARG 0.002 0.000 ARG D 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 144 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7694 (mtt180) REVERT: E 116 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.6818 (mp10) REVERT: W 70 SER cc_start: 0.8886 (p) cc_final: 0.8468 (m) REVERT: W 103 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7845 (mt-10) REVERT: W 131 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: X 9 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8186 (mm-40) outliers start: 29 outliers final: 23 residues processed: 115 average time/residue: 0.2176 time to fit residues: 33.9654 Evaluate side-chains 115 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8624 Z= 0.207 Angle : 0.447 4.946 11774 Z= 0.238 Chirality : 0.045 0.144 1505 Planarity : 0.003 0.026 1554 Dihedral : 5.007 46.183 1255 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.88 % Allowed : 12.15 % Favored : 84.97 % 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: -0.07 (0.22), residues: 1190 helix: -0.35 (0.75), residues: 56 sheet: 1.33 (0.32), residues: 224 loop : -0.39 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE E 55 TYR 0.010 0.002 TYR W 71 ARG 0.002 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7239 (mt-10) REVERT: D 144 ARG cc_start: 0.7920 (mtp180) cc_final: 0.7687 (mtt180) REVERT: E 116 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.6863 (mp10) REVERT: W 70 SER cc_start: 0.8857 (p) cc_final: 0.8566 (m) REVERT: W 103 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7884 (mt-10) REVERT: W 131 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7652 (mt0) REVERT: X 9 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8282 (mm-40) outliers start: 27 outliers final: 23 residues processed: 116 average time/residue: 0.2194 time to fit residues: 35.1764 Evaluate side-chains 121 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain X residue 70 SER Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 96 optimal weight: 0.0370 chunk 101 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 0.0970 chunk 68 optimal weight: 8.9990 overall best weight: 1.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8624 Z= 0.146 Angle : 0.414 4.683 11774 Z= 0.220 Chirality : 0.044 0.140 1505 Planarity : 0.002 0.025 1554 Dihedral : 4.690 43.062 1255 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.92 % Allowed : 13.75 % Favored : 84.33 % 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: 0.12 (0.22), residues: 1190 helix: -0.25 (0.76), residues: 56 sheet: 1.46 (0.32), residues: 224 loop : -0.26 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE E 55 TYR 0.010 0.001 TYR W 71 ARG 0.002 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7154 (mt-10) REVERT: D 144 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7654 (mtt180) REVERT: E 106 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7740 (mtpp) REVERT: W 70 SER cc_start: 0.8776 (p) cc_final: 0.8565 (m) REVERT: W 131 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7808 (mm-40) REVERT: X 9 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8055 (mt0) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.2228 time to fit residues: 33.4463 Evaluate side-chains 111 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8624 Z= 0.223 Angle : 0.452 5.064 11774 Z= 0.241 Chirality : 0.045 0.141 1505 Planarity : 0.003 0.025 1554 Dihedral : 4.901 46.596 1253 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.24 % Allowed : 13.43 % Favored : 84.33 % 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: 0.12 (0.22), residues: 1190 helix: -0.30 (0.75), residues: 56 sheet: 1.49 (0.32), residues: 224 loop : -0.27 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE E 55 TYR 0.010 0.002 TYR W 71 ARG 0.002 0.000 ARG C 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7160 (mt-10) REVERT: D 144 ARG cc_start: 0.7906 (mtp180) cc_final: 0.7652 (mtt180) REVERT: E 116 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.6863 (mp10) REVERT: W 70 SER cc_start: 0.8876 (p) cc_final: 0.8569 (m) REVERT: W 131 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: X 9 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8127 (mm-40) outliers start: 21 outliers final: 18 residues processed: 107 average time/residue: 0.2340 time to fit residues: 34.0235 Evaluate side-chains 114 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain X residue 98 VAL Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.093774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.081929 restraints weight = 10856.614| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 1.37 r_work: 0.2615 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 8624 Z= 0.455 Angle : 0.576 5.580 11774 Z= 0.309 Chirality : 0.048 0.149 1505 Planarity : 0.003 0.028 1554 Dihedral : 5.653 53.939 1253 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.56 % Allowed : 13.01 % Favored : 84.43 % 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: -0.17 (0.22), residues: 1190 helix: -0.43 (0.74), residues: 56 sheet: 1.25 (0.32), residues: 224 loop : -0.46 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE E 55 TYR 0.011 0.002 TYR C 138 ARG 0.004 0.001 ARG D 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.16 seconds wall clock time: 31 minutes 56.28 seconds (1916.28 seconds total)