Starting phenix.real_space_refine on Wed Mar 12 22:37:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eht_28152/03_2025/8eht_28152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eht_28152/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8eht_28152/03_2025/8eht_28152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eht_28152/03_2025/8eht_28152.map" model { file = "/net/cci-nas-00/data/ceres_data/8eht_28152/03_2025/8eht_28152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eht_28152/03_2025/8eht_28152.cif" } 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. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.37, per 1000 atoms: 0.63 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: 1.94 Conformation dependent library (CDL) restraints added in 1.2 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: 1.01 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: 2.04 Time building geometry restraints manager: 2.32 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: 0.01 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: 0.640 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.790 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.959 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: 0.1879 time to fit residues: 54.8474 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 : 0.996 ------------------------------------------------------------------------------- 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: 10.0000 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN F 53 GLN D 142 GLN E 13 ASN W 9 GLN B 9 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.097271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.085043 restraints weight = 10712.627| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.41 r_work: 0.2676 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8624 Z= 0.214 Angle : 0.504 5.520 11774 Z= 0.274 Chirality : 0.046 0.149 1505 Planarity : 0.003 0.025 1554 Dihedral : 5.447 44.120 1255 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.39 % Allowed : 6.08 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1190 helix: -1.04 (0.72), residues: 56 sheet: 0.61 (0.27), residues: 308 loop : -0.23 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE E 55 TYR 0.009 0.002 TYR W 71 ARG 0.003 0.000 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 144 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 LYS cc_start: 0.8793 (tttt) cc_final: 0.8386 (ttmm) REVERT: F 56 GLN cc_start: 0.8403 (mt0) cc_final: 0.8055 (mt0) REVERT: D 144 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7614 (mtp180) REVERT: W 70 SER cc_start: 0.9058 (p) cc_final: 0.8638 (m) REVERT: W 170 ASP cc_start: 0.8136 (t0) cc_final: 0.7866 (t0) REVERT: X 115 ASP cc_start: 0.8244 (p0) cc_final: 0.8032 (p0) REVERT: B 130 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7586 (pm20) REVERT: B 159 ASP cc_start: 0.8330 (m-30) cc_final: 0.8038 (m-30) outliers start: 13 outliers final: 11 residues processed: 139 average time/residue: 0.1904 time to fit residues: 36.9569 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 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 113 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 80 optimal weight: 0.0980 chunk 68 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 46 optimal weight: 0.0770 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 GLN D 142 GLN W 9 GLN B 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.096369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.084844 restraints weight = 10858.357| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 1.33 r_work: 0.2664 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8624 Z= 0.272 Angle : 0.505 5.612 11774 Z= 0.272 Chirality : 0.046 0.145 1505 Planarity : 0.003 0.026 1554 Dihedral : 5.260 41.957 1253 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.81 % Allowed : 7.68 % Favored : 90.51 % 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: 0.10 (0.23), residues: 1190 helix: -0.53 (0.73), residues: 56 sheet: 0.81 (0.27), residues: 322 loop : -0.17 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE E 55 TYR 0.009 0.002 TYR X 71 ARG 0.003 0.001 ARG X 136 *********************** 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 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 LYS cc_start: 0.8823 (tttt) cc_final: 0.8346 (ttmm) REVERT: C 141 THR cc_start: 0.8937 (m) cc_final: 0.8714 (p) REVERT: D 118 LEU cc_start: 0.8622 (tp) cc_final: 0.8388 (tp) REVERT: D 144 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7702 (mtt180) REVERT: W 7 SER cc_start: 0.8645 (m) cc_final: 0.8397 (p) REVERT: W 70 SER cc_start: 0.9134 (p) cc_final: 0.8644 (m) REVERT: B 130 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7468 (pm20) outliers start: 17 outliers final: 14 residues processed: 117 average time/residue: 0.2127 time to fit residues: 34.0701 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain F residue 161 THR 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 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 X residue 130 GLU Chi-restraints excluded: chain B residue 56 GLN 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 74 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- 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 = 0.2892 r_free = 0.2892 target = 0.095619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.084164 restraints weight = 10839.811| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 1.32 r_work: 0.2651 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8624 Z= 0.293 Angle : 0.505 5.558 11774 Z= 0.272 Chirality : 0.046 0.147 1505 Planarity : 0.003 0.027 1554 Dihedral : 5.270 42.653 1253 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.35 % Allowed : 8.96 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1190 helix: -0.37 (0.73), residues: 56 sheet: 1.04 (0.27), residues: 322 loop : -0.21 (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 D 17 *********************** 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 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 LYS cc_start: 0.8844 (tttt) cc_final: 0.8331 (ttmm) REVERT: D 144 ARG cc_start: 0.7930 (mtp180) cc_final: 0.7683 (mtt180) REVERT: E 106 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7953 (mtpp) REVERT: W 70 SER cc_start: 0.9139 (p) cc_final: 0.8633 (m) REVERT: W 103 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8127 (mt-10) REVERT: X 115 ASP cc_start: 0.8274 (p0) cc_final: 0.8063 (p0) REVERT: B 130 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7502 (pm20) REVERT: B 157 THR cc_start: 0.9208 (m) cc_final: 0.8824 (p) outliers start: 22 outliers final: 19 residues processed: 114 average time/residue: 0.2674 time to fit residues: 41.3049 Evaluate side-chains 122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 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 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 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 X residue 130 GLU 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 66 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.2932 r_free = 0.2932 target = 0.098653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.086819 restraints weight = 10676.773| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.37 r_work: 0.2687 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8624 Z= 0.150 Angle : 0.421 4.567 11774 Z= 0.227 Chirality : 0.044 0.142 1505 Planarity : 0.003 0.024 1554 Dihedral : 4.735 36.367 1253 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.60 % Allowed : 10.66 % Favored : 87.74 % 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: -0.26 (0.75), residues: 56 sheet: 1.37 (0.32), residues: 224 loop : -0.23 (0.19), residues: 910 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 W 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 131 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 THR cc_start: 0.8370 (m) cc_final: 0.8000 (t) REVERT: C 117 LYS cc_start: 0.8889 (tttt) cc_final: 0.8343 (ttmm) REVERT: D 144 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7634 (mtt180) REVERT: E 106 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8065 (mtpp) REVERT: W 70 SER cc_start: 0.8989 (p) cc_final: 0.8704 (m) REVERT: W 103 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8204 (mt-10) REVERT: X 115 ASP cc_start: 0.8220 (p0) cc_final: 0.7992 (p0) REVERT: B 130 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7356 (pm20) REVERT: B 157 THR cc_start: 0.9231 (m) cc_final: 0.8838 (p) outliers start: 15 outliers final: 14 residues processed: 125 average time/residue: 0.2776 time to fit residues: 46.7309 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 161 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN F 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.092193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.080260 restraints weight = 11049.168| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 1.38 r_work: 0.2593 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.055 8624 Z= 0.628 Angle : 0.672 6.616 11774 Z= 0.361 Chirality : 0.052 0.158 1505 Planarity : 0.004 0.032 1554 Dihedral : 5.957 50.929 1253 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.88 % Allowed : 11.30 % 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: -0.14 (0.22), residues: 1190 helix: -0.39 (0.73), residues: 56 sheet: 0.89 (0.27), residues: 322 loop : -0.49 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.003 PHE E 55 TYR 0.016 0.003 TYR B 85 ARG 0.006 0.001 ARG D 17 *********************** 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 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 LYS cc_start: 0.8827 (tttt) cc_final: 0.8267 (ttmm) REVERT: F 56 GLN cc_start: 0.8602 (mt0) cc_final: 0.8234 (mt0) REVERT: D 131 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8500 (mm-40) REVERT: E 106 LYS cc_start: 0.8319 (mtmm) cc_final: 0.8023 (mtpp) REVERT: W 103 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8123 (mt-10) REVERT: W 130 GLU cc_start: 0.8310 (tt0) cc_final: 0.8101 (tt0) REVERT: W 131 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: B 130 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7581 (pm20) REVERT: B 157 THR cc_start: 0.9186 (m) cc_final: 0.8808 (p) outliers start: 27 outliers final: 24 residues processed: 116 average time/residue: 0.2660 time to fit residues: 42.5850 Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 28 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 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 X residue 130 GLU Chi-restraints excluded: chain B residue 65 LEU 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 25 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 D 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.096558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.084631 restraints weight = 10683.302| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 1.37 r_work: 0.2652 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8624 Z= 0.203 Angle : 0.463 4.888 11774 Z= 0.248 Chirality : 0.045 0.147 1505 Planarity : 0.003 0.028 1554 Dihedral : 5.082 39.573 1253 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.56 % Allowed : 12.05 % Favored : 85.39 % 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: -0.11 (0.22), residues: 1190 helix: -0.32 (0.74), residues: 56 sheet: 1.24 (0.32), residues: 224 loop : -0.41 (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 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 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 LYS cc_start: 0.8958 (tttt) cc_final: 0.8354 (ttmm) REVERT: E 106 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8024 (mtpp) REVERT: E 116 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: W 70 SER cc_start: 0.9059 (p) cc_final: 0.8714 (m) REVERT: W 103 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8193 (mt-10) REVERT: W 131 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: B 130 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7402 (pm20) REVERT: B 157 THR cc_start: 0.9216 (m) cc_final: 0.8837 (p) outliers start: 24 outliers final: 20 residues processed: 114 average time/residue: 0.2144 time to fit residues: 33.6387 Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 113 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 100 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.093665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.081711 restraints weight = 11046.536| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 1.38 r_work: 0.2613 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 8624 Z= 0.444 Angle : 0.574 5.588 11774 Z= 0.307 Chirality : 0.048 0.150 1505 Planarity : 0.004 0.031 1554 Dihedral : 5.618 48.208 1253 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.56 % Allowed : 11.94 % Favored : 85.50 % 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: -0.31 (0.74), residues: 56 sheet: 0.94 (0.27), residues: 322 loop : -0.44 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE E 55 TYR 0.011 0.002 TYR C 138 ARG 0.004 0.001 ARG D 17 *********************** 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 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7438 (mt-10) REVERT: C 117 LYS cc_start: 0.8895 (tttt) cc_final: 0.8291 (ttmm) REVERT: F 56 GLN cc_start: 0.8610 (mt0) cc_final: 0.8260 (mt0) REVERT: E 106 LYS cc_start: 0.8325 (mtmm) cc_final: 0.8015 (mtpp) REVERT: E 116 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.6948 (mp10) REVERT: W 103 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8137 (mt-10) REVERT: W 130 GLU cc_start: 0.8307 (tt0) cc_final: 0.8082 (tt0) REVERT: W 131 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: B 130 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7528 (pm20) REVERT: B 157 THR cc_start: 0.9188 (m) cc_final: 0.8810 (p) outliers start: 24 outliers final: 21 residues processed: 116 average time/residue: 0.2332 time to fit residues: 36.1346 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.095948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.084402 restraints weight = 10787.210| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.31 r_work: 0.2649 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2900 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= 0.251 Angle : 0.481 5.065 11774 Z= 0.257 Chirality : 0.045 0.145 1505 Planarity : 0.003 0.029 1554 Dihedral : 5.180 43.259 1253 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.56 % Allowed : 12.15 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.23), residues: 1190 helix: -0.26 (0.74), residues: 56 sheet: 1.07 (0.27), residues: 322 loop : -0.36 (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 0.002 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 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7365 (mt-10) REVERT: C 117 LYS cc_start: 0.8962 (tttt) cc_final: 0.8362 (ttmm) REVERT: E 106 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8102 (mtpp) REVERT: E 116 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.6934 (mp10) REVERT: W 70 SER cc_start: 0.9106 (p) cc_final: 0.8640 (m) REVERT: W 103 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8148 (mt-10) REVERT: W 131 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: B 130 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7379 (pm20) REVERT: B 157 THR cc_start: 0.9217 (m) cc_final: 0.8856 (p) outliers start: 24 outliers final: 21 residues processed: 113 average time/residue: 0.2123 time to fit residues: 32.9271 Evaluate side-chains 122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 115 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.096808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.085395 restraints weight = 10730.680| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.30 r_work: 0.2668 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8624 Z= 0.210 Angle : 0.452 4.856 11774 Z= 0.241 Chirality : 0.045 0.143 1505 Planarity : 0.003 0.028 1554 Dihedral : 4.913 41.804 1253 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.56 % Allowed : 12.26 % 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: 0.22 (0.23), residues: 1190 helix: -0.14 (0.75), residues: 56 sheet: 1.23 (0.27), residues: 322 loop : -0.28 (0.20), residues: 812 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 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: 24 poor density : 105 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7286 (mt-10) REVERT: C 117 LYS cc_start: 0.8971 (tttt) cc_final: 0.8364 (ttmm) REVERT: E 106 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8070 (mtpp) REVERT: E 116 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.6909 (mp10) REVERT: W 70 SER cc_start: 0.9069 (p) cc_final: 0.8705 (m) REVERT: W 103 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8178 (mt-10) REVERT: W 131 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: X 115 ASP cc_start: 0.8344 (p0) cc_final: 0.8105 (p0) REVERT: B 130 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7320 (pm20) REVERT: B 157 THR cc_start: 0.9222 (m) cc_final: 0.8875 (p) outliers start: 24 outliers final: 22 residues processed: 119 average time/residue: 0.2130 time to fit residues: 35.0644 Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.093224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.081599 restraints weight = 11008.916| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 1.33 r_work: 0.2611 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 8624 Z= 0.505 Angle : 0.604 5.738 11774 Z= 0.323 Chirality : 0.049 0.151 1505 Planarity : 0.004 0.032 1554 Dihedral : 5.744 51.708 1253 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.67 % Allowed : 12.26 % Favored : 85.07 % 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: -0.11 (0.23), residues: 1190 helix: -0.31 (0.74), residues: 56 sheet: 0.93 (0.27), residues: 322 loop : -0.48 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.003 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: 3838.73 seconds wall clock time: 68 minutes 27.86 seconds (4107.86 seconds total)