Starting phenix.real_space_refine on Fri Aug 22 22:38:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eht_28152/08_2025/8eht_28152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eht_28152/08_2025/8eht_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 { model { file = "/net/cci-nas-00/data/ceres_data/8eht_28152/08_2025/8eht_28152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eht_28152/08_2025/8eht_28152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eht_28152/08_2025/8eht_28152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eht_28152/08_2025/8eht_28152.map" } resolution = 3.4 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= 0.009 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. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.49, per 1000 atoms: 0.29 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 - 3.00 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: 0.73 Conformation dependent library (CDL) restraints added in 476.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.21 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: 1.08 Time building geometry restraints manager: 0.99 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: 0.00 - 1.01: 10693 1.01 - 2.02: 919 2.02 - 3.04: 109 3.04 - 4.05: 45 4.05 - 5.06: 8 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 3.040 nonbonded pdb=" O ALA F 171 " pdb=" OG1 THR F 172 " model vdw 2.141 3.040 nonbonded pdb=" NZ LYS D 26 " pdb=" OD1 ASP D 28 " model vdw 2.167 3.120 nonbonded pdb=" O ALA E 171 " pdb=" OG1 THR E 172 " model vdw 2.193 3.040 nonbonded pdb=" O ALA D 171 " pdb=" OG1 THR D 172 " model vdw 2.212 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 8.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.280 ------------------------------------------------------------------------------- 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 8631 Z= 0.278 Angle : 0.636 5.058 11788 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG D 136 TYR 0.012 0.002 TYR E 138 PHE 0.010 0.002 PHE D 55 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 8624) covalent geometry : angle 0.63536 (11774) SS BOND : bond 0.00268 ( 7) SS BOND : angle 1.00846 ( 14) hydrogen bonds : bond 0.22960 ( 281) hydrogen bonds : angle 10.42008 ( 714) *********************** 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 to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.243 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: 0.0719 time to fit residues: 21.3466 Evaluate side-chains 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 108 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- 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 5 ASN E 13 ASN W 9 GLN B 9 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.095934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.083648 restraints weight = 10899.330| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 1.42 r_work: 0.2653 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8631 Z= 0.169 Angle : 0.532 6.117 11788 Z= 0.288 Chirality : 0.047 0.152 1505 Planarity : 0.003 0.027 1554 Dihedral : 5.662 47.668 1255 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.60 % Allowed : 6.29 % Favored : 92.11 % 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 aren not related in a simple way. whole: -0.16 (0.23), residues: 1190 helix: -0.99 (0.72), residues: 56 sheet: 0.38 (0.26), residues: 322 loop : -0.20 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 136 TYR 0.010 0.002 TYR W 138 PHE 0.010 0.002 PHE E 55 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8624) covalent geometry : angle 0.53137 (11774) SS BOND : bond 0.00426 ( 7) SS BOND : angle 0.70330 ( 14) hydrogen bonds : bond 0.03046 ( 281) hydrogen bonds : angle 6.17650 ( 714) *********************** 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 to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 LYS cc_start: 0.8778 (tttt) cc_final: 0.8349 (ttmm) REVERT: F 56 GLN cc_start: 0.8442 (mt0) cc_final: 0.8099 (mt0) REVERT: D 144 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7584 (mtp180) REVERT: W 70 SER cc_start: 0.9091 (p) cc_final: 0.8640 (m) REVERT: W 170 ASP cc_start: 0.8127 (t0) cc_final: 0.7869 (t0) REVERT: X 115 ASP cc_start: 0.8298 (p0) cc_final: 0.8088 (p0) REVERT: B 130 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7571 (pm20) outliers start: 15 outliers final: 12 residues processed: 136 average time/residue: 0.0828 time to fit residues: 15.7475 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain W residue 9 GLN Chi-restraints excluded: chain W residue 28 ASP Chi-restraints excluded: chain W residue 47 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 65 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 GLN B 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.093258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.081475 restraints weight = 10881.320| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 1.38 r_work: 0.2613 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 8631 Z= 0.297 Angle : 0.626 6.581 11788 Z= 0.337 Chirality : 0.050 0.155 1505 Planarity : 0.004 0.031 1554 Dihedral : 5.869 48.914 1253 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.13 % Allowed : 8.53 % Favored : 89.34 % 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 aren not related in a simple way. whole: -0.23 (0.22), residues: 1190 helix: -0.53 (0.73), residues: 56 sheet: 0.56 (0.27), residues: 322 loop : -0.40 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 17 TYR 0.013 0.002 TYR B 85 PHE 0.015 0.003 PHE E 55 Details of bonding type rmsd covalent geometry : bond 0.00737 ( 8624) covalent geometry : angle 0.62570 (11774) SS BOND : bond 0.00450 ( 7) SS BOND : angle 1.06064 ( 14) hydrogen bonds : bond 0.03461 ( 281) hydrogen bonds : angle 6.18822 ( 714) *********************** 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 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 LYS cc_start: 0.8844 (tttt) cc_final: 0.8303 (ttmm) REVERT: F 56 GLN cc_start: 0.8587 (mt0) cc_final: 0.8264 (mt0) REVERT: F 112 ILE cc_start: 0.9009 (mm) cc_final: 0.8792 (mm) REVERT: D 144 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7704 (mtt180) REVERT: E 106 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7954 (mtpp) REVERT: W 130 GLU cc_start: 0.8284 (tt0) cc_final: 0.8056 (tt0) REVERT: B 130 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7513 (pm20) REVERT: B 157 THR cc_start: 0.9172 (m) cc_final: 0.8774 (p) outliers start: 20 outliers final: 16 residues processed: 110 average time/residue: 0.1085 time to fit residues: 15.8234 Evaluate side-chains 111 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 161 THR 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 98 VAL Chi-restraints excluded: chain E residue 143 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 63 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 0.0980 chunk 34 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 9 GLN ** 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 = 0.2911 r_free = 0.2911 target = 0.097076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.085143 restraints weight = 10949.084| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 1.39 r_work: 0.2664 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8631 Z= 0.115 Angle : 0.459 5.266 11788 Z= 0.247 Chirality : 0.045 0.145 1505 Planarity : 0.003 0.027 1554 Dihedral : 5.067 40.719 1253 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.03 % Allowed : 9.91 % Favored : 88.06 % 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 aren not related in a simple way. whole: 0.12 (0.23), residues: 1190 helix: -0.41 (0.73), residues: 56 sheet: 1.01 (0.27), residues: 322 loop : -0.26 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 17 TYR 0.009 0.001 TYR W 71 PHE 0.009 0.001 PHE E 55 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8624) covalent geometry : angle 0.45828 (11774) SS BOND : bond 0.00229 ( 7) SS BOND : angle 0.79843 ( 14) hydrogen bonds : bond 0.02250 ( 281) hydrogen bonds : angle 5.49455 ( 714) *********************** 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 131 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 ASP cc_start: 0.7908 (m-30) cc_final: 0.7699 (m-30) REVERT: C 117 LYS cc_start: 0.8851 (tttt) cc_final: 0.8314 (ttmm) REVERT: F 56 GLN cc_start: 0.8362 (mt0) cc_final: 0.8114 (mt0) REVERT: F 132 VAL cc_start: 0.9197 (p) cc_final: 0.8988 (t) REVERT: D 144 ARG cc_start: 0.7906 (mtp180) cc_final: 0.7672 (mtt180) REVERT: E 106 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7968 (mtpp) REVERT: W 70 SER cc_start: 0.9051 (p) cc_final: 0.8632 (m) REVERT: W 103 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8218 (mt-10) REVERT: X 9 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8385 (mm-40) REVERT: B 130 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7448 (pm20) REVERT: B 157 THR cc_start: 0.9216 (m) cc_final: 0.8809 (p) outliers start: 19 outliers final: 19 residues processed: 123 average time/residue: 0.0912 time to fit residues: 15.3027 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 161 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 124 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN ** X 9 GLN ** 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 = 0.2857 r_free = 0.2857 target = 0.093082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.081026 restraints weight = 11049.782| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 1.40 r_work: 0.2611 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8631 Z= 0.237 Angle : 0.549 5.871 11788 Z= 0.294 Chirality : 0.048 0.151 1505 Planarity : 0.003 0.030 1554 Dihedral : 5.520 47.809 1253 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.67 % Allowed : 11.30 % Favored : 86.03 % 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 aren not related in a simple way. whole: -0.06 (0.22), residues: 1190 helix: -0.35 (0.74), residues: 56 sheet: 0.90 (0.27), residues: 322 loop : -0.41 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 17 TYR 0.011 0.002 TYR W 71 PHE 0.013 0.002 PHE E 55 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 8624) covalent geometry : angle 0.54828 (11774) SS BOND : bond 0.00331 ( 7) SS BOND : angle 0.75667 ( 14) hydrogen bonds : bond 0.02896 ( 281) hydrogen bonds : angle 5.77763 ( 714) *********************** 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 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 LEU cc_start: 0.8346 (mt) cc_final: 0.7944 (mp) REVERT: C 67 ASP cc_start: 0.8042 (m-30) cc_final: 0.7762 (m-30) REVERT: C 117 LYS cc_start: 0.8859 (tttt) cc_final: 0.8339 (ttmm) REVERT: F 56 GLN cc_start: 0.8447 (mt0) cc_final: 0.8123 (mt0) REVERT: F 112 ILE cc_start: 0.9009 (mm) cc_final: 0.8785 (mm) REVERT: D 144 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7742 (mtt180) REVERT: E 106 LYS cc_start: 0.8304 (mtmm) cc_final: 0.8010 (mtpp) REVERT: W 70 SER cc_start: 0.9161 (p) cc_final: 0.8622 (m) REVERT: W 103 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8153 (mt-10) REVERT: W 130 GLU cc_start: 0.8283 (tt0) cc_final: 0.8057 (tt0) REVERT: W 131 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: X 9 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8471 (mm-40) REVERT: B 130 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7516 (pm20) REVERT: B 157 THR cc_start: 0.9180 (m) cc_final: 0.8785 (p) outliers start: 25 outliers final: 20 residues processed: 113 average time/residue: 0.0908 time to fit residues: 14.1584 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 161 THR Chi-restraints excluded: chain D residue 67 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 115 ASP Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain X residue 7 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN ** X 9 GLN ** 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 = 0.2869 r_free = 0.2869 target = 0.094067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.082629 restraints weight = 10930.876| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 1.31 r_work: 0.2628 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8631 Z= 0.214 Angle : 0.526 5.505 11788 Z= 0.282 Chirality : 0.047 0.148 1505 Planarity : 0.003 0.030 1554 Dihedral : 5.441 47.017 1253 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.88 % Allowed : 11.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.22), residues: 1190 helix: -0.33 (0.74), residues: 56 sheet: 0.90 (0.27), residues: 322 loop : -0.42 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 144 TYR 0.011 0.002 TYR W 71 PHE 0.013 0.002 PHE E 55 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 8624) covalent geometry : angle 0.52549 (11774) SS BOND : bond 0.00287 ( 7) SS BOND : angle 0.61749 ( 14) hydrogen bonds : bond 0.02687 ( 281) hydrogen bonds : angle 5.69577 ( 714) *********************** 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 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 LEU cc_start: 0.8438 (mt) cc_final: 0.8001 (mp) REVERT: C 67 ASP cc_start: 0.8056 (m-30) cc_final: 0.7762 (m-30) REVERT: C 117 LYS cc_start: 0.8932 (tttt) cc_final: 0.8345 (ttmm) REVERT: F 56 GLN cc_start: 0.8419 (mt0) cc_final: 0.8151 (mt0) REVERT: F 112 ILE cc_start: 0.9009 (mm) cc_final: 0.8789 (mm) REVERT: E 106 LYS cc_start: 0.8314 (mtmm) cc_final: 0.8011 (mtpp) REVERT: E 116 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: W 70 SER cc_start: 0.9147 (p) cc_final: 0.8635 (m) REVERT: W 103 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8097 (mt-10) REVERT: W 130 GLU cc_start: 0.8249 (tt0) cc_final: 0.8018 (tt0) REVERT: W 131 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: X 9 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8393 (mm-40) REVERT: B 130 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7449 (pm20) REVERT: B 157 THR cc_start: 0.9202 (m) cc_final: 0.8829 (p) outliers start: 27 outliers final: 23 residues processed: 116 average time/residue: 0.1033 time to fit residues: 16.2768 Evaluate side-chains 120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 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 121 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 115 ASP Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain X residue 7 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 50 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN ** X 9 GLN ** 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 = 0.2861 r_free = 0.2861 target = 0.093445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.081489 restraints weight = 11163.212| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 1.40 r_work: 0.2610 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8631 Z= 0.256 Angle : 0.565 5.753 11788 Z= 0.303 Chirality : 0.048 0.150 1505 Planarity : 0.003 0.031 1554 Dihedral : 5.634 50.140 1253 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.20 % Allowed : 11.94 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.22), residues: 1190 helix: -0.32 (0.74), residues: 56 sheet: 0.82 (0.27), residues: 322 loop : -0.49 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 144 TYR 0.011 0.002 TYR W 71 PHE 0.013 0.002 PHE E 55 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 8624) covalent geometry : angle 0.56481 (11774) SS BOND : bond 0.00413 ( 7) SS BOND : angle 0.86424 ( 14) hydrogen bonds : bond 0.02902 ( 281) hydrogen bonds : angle 5.83143 ( 714) *********************** 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 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 LEU cc_start: 0.8441 (mt) cc_final: 0.8016 (mp) REVERT: C 67 ASP cc_start: 0.8069 (m-30) cc_final: 0.7769 (m-30) REVERT: C 117 LYS cc_start: 0.8896 (tttt) cc_final: 0.8298 (ttmm) REVERT: F 56 GLN cc_start: 0.8497 (mt0) cc_final: 0.8217 (mt0) REVERT: F 112 ILE cc_start: 0.8983 (mm) cc_final: 0.8775 (mm) REVERT: D 131 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8063 (mm-40) REVERT: E 106 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8035 (mtpp) REVERT: E 116 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: W 103 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8116 (mt-10) REVERT: W 130 GLU cc_start: 0.8321 (tt0) cc_final: 0.8099 (tt0) REVERT: W 131 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: X 9 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8452 (mm-40) REVERT: B 130 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7507 (pm20) REVERT: B 157 THR cc_start: 0.9196 (m) cc_final: 0.8814 (p) outliers start: 30 outliers final: 25 residues processed: 117 average time/residue: 0.1016 time to fit residues: 15.9210 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 161 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 131 GLN 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 121 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 115 ASP Chi-restraints excluded: chain W residue 131 GLN 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN C 142 GLN ** X 9 GLN ** 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 = 0.2883 r_free = 0.2883 target = 0.095070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.083724 restraints weight = 10876.230| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 1.29 r_work: 0.2645 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8631 Z= 0.165 Angle : 0.488 5.380 11788 Z= 0.261 Chirality : 0.046 0.145 1505 Planarity : 0.003 0.029 1554 Dihedral : 5.245 46.008 1253 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.88 % Allowed : 12.58 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.22), residues: 1190 helix: -0.27 (0.74), residues: 56 sheet: 1.10 (0.32), residues: 224 loop : -0.54 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.011 0.002 TYR W 71 PHE 0.011 0.002 PHE E 55 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8624) covalent geometry : angle 0.48754 (11774) SS BOND : bond 0.00256 ( 7) SS BOND : angle 0.72548 ( 14) hydrogen bonds : bond 0.02418 ( 281) hydrogen bonds : angle 5.55288 ( 714) *********************** 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 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 LEU cc_start: 0.8440 (mt) cc_final: 0.7994 (mp) REVERT: C 67 ASP cc_start: 0.8063 (m-30) cc_final: 0.7781 (m-30) REVERT: C 117 LYS cc_start: 0.8902 (tttt) cc_final: 0.8320 (ttmm) REVERT: F 56 GLN cc_start: 0.8409 (mt0) cc_final: 0.8144 (mt0) REVERT: F 112 ILE cc_start: 0.9000 (mm) cc_final: 0.8773 (mm) REVERT: D 131 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7859 (mm-40) REVERT: E 106 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8113 (mtpp) REVERT: E 116 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.6889 (mp10) REVERT: W 70 SER cc_start: 0.9111 (p) cc_final: 0.8636 (m) REVERT: W 103 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8151 (mt-10) REVERT: W 131 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: X 9 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8363 (mm-40) REVERT: B 130 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7359 (pm20) REVERT: B 157 THR cc_start: 0.9205 (m) cc_final: 0.8832 (p) outliers start: 27 outliers final: 23 residues processed: 116 average time/residue: 0.0922 time to fit residues: 14.7153 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 68 ASP 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 161 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 131 GLN 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 121 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 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 143 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN ** X 9 GLN ** 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 = 0.2859 r_free = 0.2859 target = 0.093308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.081543 restraints weight = 10954.194| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 1.36 r_work: 0.2608 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 8631 Z= 0.266 Angle : 0.569 5.768 11788 Z= 0.305 Chirality : 0.048 0.149 1505 Planarity : 0.003 0.032 1554 Dihedral : 5.656 52.284 1253 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.20 % Allowed : 12.69 % Favored : 84.12 % 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 aren not related in a simple way. whole: -0.21 (0.23), residues: 1190 helix: -0.30 (0.74), residues: 56 sheet: 0.80 (0.27), residues: 322 loop : -0.53 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 17 TYR 0.011 0.002 TYR W 71 PHE 0.014 0.002 PHE E 55 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 8624) covalent geometry : angle 0.56856 (11774) SS BOND : bond 0.00389 ( 7) SS BOND : angle 0.90419 ( 14) hydrogen bonds : bond 0.02917 ( 281) hydrogen bonds : angle 5.81391 ( 714) *********************** 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 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7395 (mt-10) REVERT: C 65 LEU cc_start: 0.8451 (mt) cc_final: 0.8013 (mp) REVERT: C 67 ASP cc_start: 0.8073 (m-30) cc_final: 0.7755 (m-30) REVERT: C 117 LYS cc_start: 0.8898 (tttt) cc_final: 0.8301 (ttmm) REVERT: F 56 GLN cc_start: 0.8477 (mt0) cc_final: 0.8198 (mt0) REVERT: F 112 ILE cc_start: 0.9009 (mm) cc_final: 0.8790 (mm) REVERT: D 131 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8024 (mm-40) REVERT: E 106 LYS cc_start: 0.8390 (mtmm) cc_final: 0.8084 (mtpp) REVERT: E 116 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.6951 (mp10) REVERT: W 103 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8079 (mt-10) REVERT: W 131 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: B 130 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7410 (pm20) REVERT: B 157 THR cc_start: 0.9181 (m) cc_final: 0.8791 (p) outliers start: 30 outliers final: 27 residues processed: 115 average time/residue: 0.1025 time to fit residues: 16.0116 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 131 GLN 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 121 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 115 ASP Chi-restraints excluded: chain W residue 131 GLN 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 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 8 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN D 142 GLN ** X 9 GLN ** 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 = 0.2900 r_free = 0.2900 target = 0.096362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.084628 restraints weight = 10740.462| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 1.36 r_work: 0.2657 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8631 Z= 0.125 Angle : 0.452 5.131 11788 Z= 0.242 Chirality : 0.045 0.142 1505 Planarity : 0.003 0.029 1554 Dihedral : 5.006 45.673 1253 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.88 % Allowed : 13.01 % Favored : 84.12 % 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 aren not related in a simple way. whole: 0.03 (0.23), residues: 1190 helix: -0.21 (0.75), residues: 56 sheet: 1.04 (0.27), residues: 322 loop : -0.39 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.010 0.002 TYR W 71 PHE 0.010 0.001 PHE E 55 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8624) covalent geometry : angle 0.45200 (11774) SS BOND : bond 0.00182 ( 7) SS BOND : angle 0.61150 ( 14) hydrogen bonds : bond 0.02166 ( 281) hydrogen bonds : angle 5.36004 ( 714) ********************** 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 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7317 (mt-10) REVERT: C 65 LEU cc_start: 0.8408 (mt) cc_final: 0.7953 (mp) REVERT: C 67 ASP cc_start: 0.8062 (m-30) cc_final: 0.7772 (m-30) REVERT: C 117 LYS cc_start: 0.8930 (tttt) cc_final: 0.8302 (ttmm) REVERT: F 112 ILE cc_start: 0.8979 (mm) cc_final: 0.8742 (mm) REVERT: D 131 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7789 (mm-40) REVERT: E 106 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8140 (mtpp) REVERT: E 116 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.6859 (mp10) REVERT: W 70 SER cc_start: 0.9045 (p) cc_final: 0.8709 (m) REVERT: W 103 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8207 (mt-10) REVERT: W 131 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7820 (mm-40) REVERT: X 9 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8346 (mt0) REVERT: B 157 THR cc_start: 0.9207 (m) cc_final: 0.8817 (p) outliers start: 27 outliers final: 23 residues processed: 119 average time/residue: 0.0945 time to fit residues: 15.5080 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 68 ASP 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 161 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 131 GLN 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 121 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 GLN ** X 9 GLN ** 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 = 0.2887 r_free = 0.2887 target = 0.095330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.083630 restraints weight = 10806.370| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 1.35 r_work: 0.2642 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8631 Z= 0.169 Angle : 0.486 5.420 11788 Z= 0.260 Chirality : 0.046 0.142 1505 Planarity : 0.003 0.030 1554 Dihedral : 5.166 48.781 1253 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.77 % Allowed : 13.54 % Favored : 83.69 % 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 aren not related in a simple way. whole: 0.07 (0.23), residues: 1190 helix: -0.17 (0.75), residues: 56 sheet: 1.08 (0.28), residues: 322 loop : -0.36 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.011 0.002 TYR W 71 PHE 0.011 0.002 PHE E 55 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8624) covalent geometry : angle 0.48587 (11774) SS BOND : bond 0.00258 ( 7) SS BOND : angle 0.68195 ( 14) hydrogen bonds : bond 0.02434 ( 281) hydrogen bonds : angle 5.45531 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1633.92 seconds wall clock time: 28 minutes 46.51 seconds (1726.51 seconds total)