Starting phenix.real_space_refine on Sat Jul 26 04:57:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eht_28152/07_2025/8eht_28152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eht_28152/07_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_28152/07_2025/8eht_28152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eht_28152/07_2025/8eht_28152.map" model { file = "/net/cci-nas-00/data/ceres_data/8eht_28152/07_2025/8eht_28152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eht_28152/07_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-5711/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: 5.11, per 1000 atoms: 0.60 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 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: 1.97 Time building geometry restraints manager: 2.33 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.310 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.22960 ( 281) hydrogen bonds : angle 10.42008 ( 714) SS BOND : bond 0.00268 ( 7) SS BOND : angle 1.00846 ( 14) covalent geometry : bond 0.00620 ( 8624) covalent geometry : angle 0.63536 (11774) *********************** 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 : 0.986 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: 0.1882 time to fit residues: 55.0275 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 : 0.961 ------------------------------------------------------------------------------- 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: 2.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 F 79 ASN D 142 GLN E 13 ASN W 9 GLN B 9 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.098320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.086160 restraints weight = 10624.749| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 1.40 r_work: 0.2696 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8631 Z= 0.117 Angle : 0.490 5.442 11788 Z= 0.265 Chirality : 0.046 0.148 1505 Planarity : 0.003 0.025 1554 Dihedral : 5.393 44.032 1255 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.17 % Allowed : 6.18 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1190 helix: -1.05 (0.72), residues: 56 sheet: 0.63 (0.27), residues: 308 loop : -0.20 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE C 55 TYR 0.009 0.001 TYR W 71 ARG 0.002 0.000 ARG X 136 Details of bonding type rmsd hydrogen bonds : bond 0.02560 ( 281) hydrogen bonds : angle 6.02639 ( 714) SS BOND : bond 0.00283 ( 7) SS BOND : angle 0.58235 ( 14) covalent geometry : bond 0.00270 ( 8624) covalent geometry : angle 0.48948 (11774) *********************** 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 146 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 LYS cc_start: 0.8786 (tttt) cc_final: 0.8384 (ttmm) REVERT: F 79 ASN cc_start: 0.7580 (m-40) cc_final: 0.7368 (p0) REVERT: D 144 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7601 (mtp180) REVERT: W 70 SER cc_start: 0.9033 (p) cc_final: 0.8642 (m) REVERT: W 170 ASP cc_start: 0.8158 (t0) cc_final: 0.7900 (t0) REVERT: X 115 ASP cc_start: 0.8230 (p0) cc_final: 0.8009 (p0) REVERT: B 130 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7502 (pm20) REVERT: B 159 ASP cc_start: 0.8328 (m-30) cc_final: 0.8040 (m-30) outliers start: 11 outliers final: 9 residues processed: 141 average time/residue: 0.1920 time to fit residues: 37.7441 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 98 VAL Chi-restraints excluded: chain W residue 9 GLN Chi-restraints excluded: chain W residue 28 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 113 optimal weight: 0.0980 chunk 105 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 0.0470 chunk 80 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 46 optimal weight: 0.0970 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.3678 ------------------------------------------------------------------------------- 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 E 9 GLN W 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.099146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.087054 restraints weight = 10735.387| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.40 r_work: 0.2703 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8631 Z= 0.098 Angle : 0.438 4.950 11788 Z= 0.236 Chirality : 0.045 0.139 1505 Planarity : 0.003 0.024 1554 Dihedral : 4.849 37.463 1253 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.49 % Allowed : 7.36 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1190 helix: -0.48 (0.74), residues: 56 sheet: 1.15 (0.27), residues: 308 loop : -0.11 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE E 55 TYR 0.008 0.001 TYR W 71 ARG 0.002 0.000 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.02309 ( 281) hydrogen bonds : angle 5.48553 ( 714) SS BOND : bond 0.00187 ( 7) SS BOND : angle 0.60571 ( 14) covalent geometry : bond 0.00226 ( 8624) covalent geometry : angle 0.43759 (11774) *********************** 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 139 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 THR cc_start: 0.8354 (m) cc_final: 0.8040 (t) REVERT: C 117 LYS cc_start: 0.8788 (tttt) cc_final: 0.8301 (ttmm) REVERT: D 118 LEU cc_start: 0.8531 (tp) cc_final: 0.8286 (tp) REVERT: D 144 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7538 (mtp180) REVERT: E 106 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7842 (mtpp) REVERT: W 70 SER cc_start: 0.9035 (p) cc_final: 0.8651 (m) REVERT: W 103 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8218 (mt-10) REVERT: X 9 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8330 (mm-40) REVERT: X 115 ASP cc_start: 0.8223 (p0) cc_final: 0.8022 (p0) REVERT: B 130 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7393 (pm20) REVERT: B 159 ASP cc_start: 0.8204 (m-30) cc_final: 0.7958 (m-30) outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.1931 time to fit residues: 35.9232 Evaluate side-chains 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain W residue 47 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 142 GLN ** X 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.093658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.081780 restraints weight = 10995.943| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 1.39 r_work: 0.2613 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8631 Z= 0.288 Angle : 0.603 6.045 11788 Z= 0.324 Chirality : 0.049 0.155 1505 Planarity : 0.004 0.030 1554 Dihedral : 5.731 47.159 1253 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.35 % Allowed : 9.28 % Favored : 88.38 % 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: 0.04 (0.22), residues: 1190 helix: -0.38 (0.73), residues: 56 sheet: 0.88 (0.27), residues: 322 loop : -0.27 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.003 PHE E 55 TYR 0.012 0.002 TYR B 85 ARG 0.005 0.001 ARG X 136 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 281) hydrogen bonds : angle 5.97472 ( 714) SS BOND : bond 0.00388 ( 7) SS BOND : angle 0.82365 ( 14) covalent geometry : bond 0.00716 ( 8624) covalent geometry : angle 0.60220 (11774) *********************** 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 128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 ASP cc_start: 0.8000 (m-30) cc_final: 0.7776 (m-30) REVERT: C 117 LYS cc_start: 0.8852 (tttt) cc_final: 0.8311 (ttmm) REVERT: F 56 GLN cc_start: 0.8487 (mt0) cc_final: 0.8147 (mt0) REVERT: F 112 ILE cc_start: 0.8979 (mm) cc_final: 0.8765 (mm) REVERT: D 144 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7702 (mtt180) REVERT: E 106 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7968 (mtpp) REVERT: W 130 GLU cc_start: 0.8294 (tt0) cc_final: 0.8068 (tt0) REVERT: B 130 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7509 (pm20) REVERT: B 157 THR cc_start: 0.9166 (m) cc_final: 0.8764 (p) outliers start: 22 outliers final: 21 residues processed: 118 average time/residue: 0.2285 time to fit residues: 36.4370 Evaluate side-chains 122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 28 ASP 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 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 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: 8.9990 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.2886 r_free = 0.2886 target = 0.095252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.083768 restraints weight = 10861.846| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 1.31 r_work: 0.2643 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2628 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= 0.182 Angle : 0.506 5.328 11788 Z= 0.271 Chirality : 0.046 0.148 1505 Planarity : 0.003 0.029 1554 Dihedral : 5.315 42.861 1253 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.13 % Allowed : 10.34 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1190 helix: -0.39 (0.73), residues: 56 sheet: 1.10 (0.32), residues: 224 loop : -0.48 (0.18), residues: 910 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 0.002 0.000 ARG X 136 Details of bonding type rmsd hydrogen bonds : bond 0.02580 ( 281) hydrogen bonds : angle 5.65930 ( 714) SS BOND : bond 0.00255 ( 7) SS BOND : angle 0.85231 ( 14) covalent geometry : bond 0.00444 ( 8624) covalent geometry : angle 0.50495 (11774) *********************** 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 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 ASP cc_start: 0.7940 (m-30) cc_final: 0.7659 (m-30) REVERT: C 117 LYS cc_start: 0.8812 (tttt) cc_final: 0.8303 (ttmm) REVERT: F 112 ILE cc_start: 0.8988 (mm) cc_final: 0.8755 (mm) REVERT: D 144 ARG cc_start: 0.7930 (mtp180) cc_final: 0.7687 (mtt180) REVERT: E 106 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7973 (mtpp) REVERT: W 70 SER cc_start: 0.9135 (p) cc_final: 0.8653 (m) REVERT: W 103 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8126 (mt-10) REVERT: X 9 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8378 (mm-40) REVERT: B 130 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7468 (pm20) REVERT: B 157 THR cc_start: 0.9199 (m) cc_final: 0.8833 (p) outliers start: 20 outliers final: 20 residues processed: 111 average time/residue: 0.2434 time to fit residues: 37.6138 Evaluate side-chains 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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 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 X residue 130 GLU 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: 3.9990 chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 71 optimal weight: 0.0980 chunk 82 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 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 = 0.2916 r_free = 0.2916 target = 0.097433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.085599 restraints weight = 10730.524| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.37 r_work: 0.2671 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2756 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= 0.117 Angle : 0.438 4.735 11788 Z= 0.235 Chirality : 0.044 0.142 1505 Planarity : 0.003 0.027 1554 Dihedral : 4.857 38.169 1253 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.13 % Allowed : 11.30 % Favored : 86.57 % 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: -0.04 (0.22), residues: 1190 helix: -0.22 (0.74), residues: 56 sheet: 1.26 (0.32), residues: 224 loop : -0.36 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE E 55 TYR 0.010 0.002 TYR W 71 ARG 0.002 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.02153 ( 281) hydrogen bonds : angle 5.28610 ( 714) SS BOND : bond 0.00204 ( 7) SS BOND : angle 0.59296 ( 14) covalent geometry : bond 0.00276 ( 8624) covalent geometry : angle 0.43791 (11774) *********************** 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 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 ASP cc_start: 0.7913 (m-30) cc_final: 0.7630 (m-30) REVERT: C 117 LYS cc_start: 0.8941 (tttt) cc_final: 0.8350 (ttmm) REVERT: F 112 ILE cc_start: 0.8973 (mm) cc_final: 0.8726 (mm) REVERT: F 142 GLN cc_start: 0.8715 (mt0) cc_final: 0.8459 (mt0) REVERT: D 144 ARG cc_start: 0.7891 (mtp180) cc_final: 0.7651 (mtt180) REVERT: E 106 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8090 (mtpp) REVERT: W 70 SER cc_start: 0.9027 (p) cc_final: 0.8710 (m) REVERT: W 103 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8191 (mt-10) REVERT: X 9 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8311 (mm-40) REVERT: X 115 ASP cc_start: 0.8280 (p0) cc_final: 0.8037 (p0) REVERT: X 124 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7587 (mttt) REVERT: B 130 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7364 (pm20) REVERT: B 157 THR cc_start: 0.9217 (m) cc_final: 0.8849 (p) outliers start: 20 outliers final: 17 residues processed: 116 average time/residue: 0.3410 time to fit residues: 57.4714 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 2.761 ------------------------------------------------------------------------------- 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 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 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 25 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.0270 chunk 118 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- 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 = 0.2893 r_free = 0.2893 target = 0.095913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.084480 restraints weight = 10794.736| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 1.31 r_work: 0.2658 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.004 0.029 8631 Z= 0.164 Angle : 0.478 5.093 11788 Z= 0.256 Chirality : 0.045 0.145 1505 Planarity : 0.003 0.028 1554 Dihedral : 5.076 41.933 1253 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -0.01 (0.22), residues: 1190 helix: -0.21 (0.75), residues: 56 sheet: 1.30 (0.32), residues: 224 loop : -0.34 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE E 55 TYR 0.010 0.002 TYR W 71 ARG 0.002 0.000 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.02455 ( 281) hydrogen bonds : angle 5.41877 ( 714) SS BOND : bond 0.00252 ( 7) SS BOND : angle 0.57976 ( 14) covalent geometry : bond 0.00399 ( 8624) covalent geometry : angle 0.47766 (11774) *********************** 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 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 ASP cc_start: 0.7916 (m-30) cc_final: 0.7645 (m-30) REVERT: C 117 LYS cc_start: 0.8959 (tttt) cc_final: 0.8374 (ttmm) REVERT: F 112 ILE cc_start: 0.8974 (mm) cc_final: 0.8757 (mm) REVERT: D 131 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8344 (mm-40) REVERT: D 144 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7708 (mtt180) REVERT: E 106 LYS cc_start: 0.8295 (mtmm) cc_final: 0.8000 (mtpp) REVERT: E 116 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: W 70 SER cc_start: 0.9090 (p) cc_final: 0.8610 (m) REVERT: W 103 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8140 (mt-10) REVERT: W 131 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: X 9 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8363 (mm-40) REVERT: X 115 ASP cc_start: 0.8309 (p0) cc_final: 0.8055 (p0) REVERT: B 130 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7445 (pm20) REVERT: B 157 THR cc_start: 0.9212 (m) cc_final: 0.8859 (p) outliers start: 24 outliers final: 18 residues processed: 115 average time/residue: 0.2754 time to fit residues: 43.8350 Evaluate side-chains 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 113 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.2848 r_free = 0.2848 target = 0.092571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.080476 restraints weight = 11129.750| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 1.40 r_work: 0.2605 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2807 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= 0.286 Angle : 0.585 5.473 11788 Z= 0.315 Chirality : 0.049 0.151 1505 Planarity : 0.004 0.031 1554 Dihedral : 5.697 48.733 1253 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -0.03 (0.23), residues: 1190 helix: -0.36 (0.73), residues: 56 sheet: 0.91 (0.27), residues: 322 loop : -0.38 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 281) hydrogen bonds : angle 5.80501 ( 714) SS BOND : bond 0.00398 ( 7) SS BOND : angle 0.77514 ( 14) covalent geometry : bond 0.00707 ( 8624) covalent geometry : angle 0.58510 (11774) *********************** 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 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 LEU cc_start: 0.8386 (mt) cc_final: 0.7955 (mp) REVERT: C 67 ASP cc_start: 0.8015 (m-30) cc_final: 0.7726 (m-30) REVERT: C 117 LYS cc_start: 0.8901 (tttt) cc_final: 0.8300 (ttmm) REVERT: F 56 GLN cc_start: 0.8565 (mt0) cc_final: 0.8213 (mt0) REVERT: F 112 ILE cc_start: 0.9010 (mm) cc_final: 0.8787 (mm) REVERT: E 106 LYS cc_start: 0.8324 (mtmm) cc_final: 0.7999 (mtpp) REVERT: E 116 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.6986 (mp10) REVERT: W 103 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8099 (mt-10) REVERT: W 130 GLU cc_start: 0.8321 (tt0) cc_final: 0.8099 (tt0) REVERT: W 131 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: X 9 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8422 (mm-40) REVERT: B 130 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7485 (pm20) REVERT: B 157 THR cc_start: 0.9188 (m) cc_final: 0.8826 (p) outliers start: 24 outliers final: 21 residues processed: 115 average time/residue: 0.2420 time to fit residues: 37.2388 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 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 = 0.2898 r_free = 0.2898 target = 0.096246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.084814 restraints weight = 10844.891| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 1.31 r_work: 0.2658 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8631 Z= 0.136 Angle : 0.463 4.892 11788 Z= 0.249 Chirality : 0.045 0.146 1505 Planarity : 0.003 0.028 1554 Dihedral : 5.067 41.714 1253 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.24 % Allowed : 12.58 % 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: -0.09 (0.22), residues: 1190 helix: -0.27 (0.74), residues: 56 sheet: 1.21 (0.32), residues: 224 loop : -0.39 (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 F 71 ARG 0.002 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.02252 ( 281) hydrogen bonds : angle 5.41031 ( 714) SS BOND : bond 0.00167 ( 7) SS BOND : angle 0.85927 ( 14) covalent geometry : bond 0.00324 ( 8624) covalent geometry : angle 0.46246 (11774) *********************** 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 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 ASP cc_start: 0.8019 (m-30) cc_final: 0.7737 (m-30) REVERT: C 117 LYS cc_start: 0.8976 (tttt) cc_final: 0.8373 (ttmm) REVERT: F 112 ILE cc_start: 0.8978 (mm) cc_final: 0.8754 (mm) REVERT: E 106 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8015 (mtpp) REVERT: E 116 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.6906 (mp10) REVERT: W 70 SER cc_start: 0.9070 (p) cc_final: 0.8710 (m) REVERT: W 103 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8138 (mt-10) REVERT: W 131 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: X 9 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8359 (mm-40) REVERT: B 130 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7362 (pm20) REVERT: B 157 THR cc_start: 0.9211 (m) cc_final: 0.8855 (p) outliers start: 21 outliers final: 19 residues processed: 113 average time/residue: 0.2068 time to fit residues: 32.4361 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 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 74 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.2889 r_free = 0.2889 target = 0.095502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.083714 restraints weight = 10828.872| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 1.36 r_work: 0.2643 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8631 Z= 0.184 Angle : 0.508 8.402 11788 Z= 0.271 Chirality : 0.046 0.150 1505 Planarity : 0.003 0.029 1554 Dihedral : 5.242 44.432 1253 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.77 % Allowed : 12.26 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1190 helix: -0.25 (0.75), residues: 56 sheet: 1.18 (0.32), residues: 224 loop : -0.41 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE E 55 TYR 0.010 0.002 TYR W 71 ARG 0.003 0.001 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.02542 ( 281) hydrogen bonds : angle 5.52972 ( 714) SS BOND : bond 0.00619 ( 7) SS BOND : angle 1.01587 ( 14) covalent geometry : bond 0.00448 ( 8624) covalent geometry : angle 0.50690 (11774) ********************** 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 120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 LEU cc_start: 0.8426 (mt) cc_final: 0.7975 (mp) REVERT: C 67 ASP cc_start: 0.8076 (m-30) cc_final: 0.7780 (m-30) REVERT: C 117 LYS cc_start: 0.8972 (tttt) cc_final: 0.8368 (ttmm) REVERT: F 112 ILE cc_start: 0.9007 (mm) cc_final: 0.8764 (mm) REVERT: E 106 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8026 (mtpp) REVERT: E 116 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: W 70 SER cc_start: 0.9121 (p) cc_final: 0.8620 (m) REVERT: W 103 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8130 (mt-10) REVERT: W 131 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7770 (mt0) REVERT: X 9 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8317 (mm-40) REVERT: B 130 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7408 (pm20) REVERT: B 157 THR cc_start: 0.9205 (m) cc_final: 0.8854 (p) outliers start: 26 outliers final: 21 residues processed: 111 average time/residue: 0.2277 time to fit residues: 35.0424 Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 45 GLU 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 115 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.2844 r_free = 0.2844 target = 0.092290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.080191 restraints weight = 11126.939| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 1.41 r_work: 0.2604 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 8631 Z= 0.308 Angle : 0.623 11.617 11788 Z= 0.332 Chirality : 0.050 0.151 1505 Planarity : 0.004 0.032 1554 Dihedral : 5.820 52.738 1253 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.35 % Allowed : 12.69 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1190 helix: -0.39 (0.73), residues: 56 sheet: 0.84 (0.27), residues: 322 loop : -0.48 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE E 55 TYR 0.011 0.002 TYR C 138 ARG 0.005 0.001 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 281) hydrogen bonds : angle 5.88449 ( 714) SS BOND : bond 0.00726 ( 7) SS BOND : angle 1.66272 ( 14) covalent geometry : bond 0.00760 ( 8624) covalent geometry : angle 0.62040 (11774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4141.61 seconds wall clock time: 74 minutes 28.27 seconds (4468.27 seconds total)