Starting phenix.real_space_refine on Tue Mar 3 10:50:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f29_31428/03_2026/7f29_31428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f29_31428/03_2026/7f29_31428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f29_31428/03_2026/7f29_31428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f29_31428/03_2026/7f29_31428.map" model { file = "/net/cci-nas-00/data/ceres_data/7f29_31428/03_2026/7f29_31428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f29_31428/03_2026/7f29_31428.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 6 5.16 5 C 1140 2.51 5 N 288 2.21 5 O 360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1794 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GAL': 1, 'X6X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: C, D, F, A, B, H, I, J, K, L Time building chain proxies: 0.45, per 1000 atoms: 0.25 Number of scatterers: 1794 At special positions: 0 Unit cell: (56.18, 125.08, 33.92, 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 6 16.00 O 360 8.00 N 288 7.00 C 1140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Links applied BETA1-3 " X6X G 1 " - " GAL G 2 " " X6X H 1 " - " GAL H 2 " " X6X I 1 " - " GAL I 2 " " X6X J 1 " - " GAL J 2 " " X6X K 1 " - " GAL K 2 " " X6X L 1 " - " GAL L 2 " Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 80.5 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 372 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 54.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 11 through 12 removed outlier: 7.209A pdb=" N GLU E 11 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 27 removed outlier: 6.968A pdb=" N LYS C 16 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU E 17 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 18 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE E 19 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE C 20 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA E 21 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU C 22 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER C 26 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN E 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LYS E 16 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N PHE D 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N VAL E 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA D 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N PHE E 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N ASP D 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU E 22 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY D 25 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N VAL E 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN D 27 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N SER E 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 30 through 35 removed outlier: 6.927A pdb=" N ILE E 31 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 32 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY E 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N ALA E 30 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N GLY D 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE E 32 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N MET D 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 41 removed outlier: 6.727A pdb=" N VAL E 40 " --> pdb=" O ILE C 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.210A pdb=" N GLU F 11 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 15 through 27 removed outlier: 6.967A pdb=" N LYS A 16 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU F 17 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 18 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE F 19 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE A 20 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA F 21 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A 22 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER A 26 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN F 27 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N LYS F 16 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N PHE B 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL F 18 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA B 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N PHE F 20 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N ASP B 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU F 22 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY B 25 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N VAL F 24 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASN B 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N SER F 26 " --> pdb=" O ASN B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.927A pdb=" N ILE F 31 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE A 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY F 33 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N ALA F 30 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N GLY B 33 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE F 32 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N MET B 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU F 34 " --> pdb=" O MET B 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.726A pdb=" N VAL F 40 " --> pdb=" O ILE A 41 " (cutoff:3.500A) 16 hydrogen bonds defined for protein. 48 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: 0.21 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 301 1.32 - 1.44: 449 1.44 - 1.56: 1056 1.56 - 1.68: 0 1.68 - 1.80: 12 Bond restraints: 1818 Sorted by residual: bond pdb=" C3 X6X H 1 " pdb=" O3 X6X H 1 " ideal model delta sigma weight residual 1.410 1.511 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C3 X6X K 1 " pdb=" O3 X6X K 1 " ideal model delta sigma weight residual 1.410 1.510 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C3 X6X L 1 " pdb=" O3 X6X L 1 " ideal model delta sigma weight residual 1.410 1.510 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C3 X6X I 1 " pdb=" O3 X6X I 1 " ideal model delta sigma weight residual 1.410 1.510 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C3 X6X G 1 " pdb=" O3 X6X G 1 " ideal model delta sigma weight residual 1.410 1.510 -0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 1813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 2183 1.35 - 2.70: 127 2.70 - 4.05: 84 4.05 - 5.40: 36 5.40 - 6.74: 6 Bond angle restraints: 2436 Sorted by residual: angle pdb=" C3 GAL I 2 " pdb=" C4 GAL I 2 " pdb=" C5 GAL I 2 " ideal model delta sigma weight residual 107.77 114.51 -6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" C3 GAL J 2 " pdb=" C4 GAL J 2 " pdb=" C5 GAL J 2 " ideal model delta sigma weight residual 107.77 114.50 -6.73 3.00e+00 1.11e-01 5.04e+00 angle pdb=" C3 GAL H 2 " pdb=" C4 GAL H 2 " pdb=" C5 GAL H 2 " ideal model delta sigma weight residual 107.77 114.49 -6.72 3.00e+00 1.11e-01 5.01e+00 angle pdb=" C3 GAL K 2 " pdb=" C4 GAL K 2 " pdb=" C5 GAL K 2 " ideal model delta sigma weight residual 107.77 114.48 -6.71 3.00e+00 1.11e-01 5.00e+00 angle pdb=" C3 GAL G 2 " pdb=" C4 GAL G 2 " pdb=" C5 GAL G 2 " ideal model delta sigma weight residual 107.77 114.47 -6.70 3.00e+00 1.11e-01 5.00e+00 ... (remaining 2431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 1046 16.94 - 33.88: 106 33.88 - 50.82: 6 50.82 - 67.76: 6 67.76 - 84.70: 6 Dihedral angle restraints: 1170 sinusoidal: 582 harmonic: 588 Sorted by residual: dihedral pdb=" CB GLU B 22 " pdb=" CG GLU B 22 " pdb=" CD GLU B 22 " pdb=" OE1 GLU B 22 " ideal model delta sinusoidal sigma weight residual 0.00 84.70 -84.70 1 3.00e+01 1.11e-03 9.68e+00 dihedral pdb=" CB GLU C 22 " pdb=" CG GLU C 22 " pdb=" CD GLU C 22 " pdb=" OE1 GLU C 22 " ideal model delta sinusoidal sigma weight residual 0.00 84.70 -84.70 1 3.00e+01 1.11e-03 9.68e+00 dihedral pdb=" CB GLU D 22 " pdb=" CG GLU D 22 " pdb=" CD GLU D 22 " pdb=" OE1 GLU D 22 " ideal model delta sinusoidal sigma weight residual 0.00 84.69 -84.69 1 3.00e+01 1.11e-03 9.68e+00 ... (remaining 1167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 182 0.029 - 0.058: 31 0.058 - 0.087: 22 0.087 - 0.116: 56 0.116 - 0.145: 21 Chirality restraints: 312 Sorted by residual: chirality pdb=" C1 GAL I 2 " pdb=" O3 X6X I 1 " pdb=" C2 GAL I 2 " pdb=" O5 GAL I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.90e+00 chirality pdb=" C1 GAL G 2 " pdb=" O3 X6X G 1 " pdb=" C2 GAL G 2 " pdb=" O5 GAL G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.87e+00 chirality pdb=" C1 GAL J 2 " pdb=" O3 X6X J 1 " pdb=" C2 GAL J 2 " pdb=" O5 GAL J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.53e+00 ... (remaining 309 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 20 " -0.008 2.00e-02 2.50e+03 6.37e-03 7.10e-01 pdb=" CG PHE A 20 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 20 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 20 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 20 " -0.008 2.00e-02 2.50e+03 6.25e-03 6.84e-01 pdb=" CG PHE F 20 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE F 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 20 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 20 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " -0.008 2.00e-02 2.50e+03 6.20e-03 6.73e-01 pdb=" CG PHE B 20 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " -0.002 2.00e-02 2.50e+03 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 492 2.82 - 3.34: 1454 3.34 - 3.86: 2820 3.86 - 4.38: 2966 4.38 - 4.90: 5932 Nonbonded interactions: 13664 Sorted by model distance: nonbonded pdb=" OE2 GLU A 11 " pdb=" NE2 HIS A 13 " model vdw 2.305 3.120 nonbonded pdb=" OE2 GLU E 11 " pdb=" NE2 HIS E 13 " model vdw 2.305 3.120 nonbonded pdb=" OE2 GLU B 11 " pdb=" NE2 HIS B 13 " model vdw 2.306 3.120 nonbonded pdb=" OE2 GLU D 11 " pdb=" NE2 HIS D 13 " model vdw 2.306 3.120 nonbonded pdb=" OE2 GLU F 11 " pdb=" NE2 HIS F 13 " model vdw 2.306 3.120 ... (remaining 13659 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 'E' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.650 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.270 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.014 0.101 1836 Z= 0.700 Angle : 1.073 6.744 2454 Z= 0.450 Chirality : 0.061 0.145 312 Planarity : 0.002 0.006 288 Dihedral : 14.683 84.703 798 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.42), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.32), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.003 TYR E 10 PHE 0.014 0.003 PHE A 20 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.01381 ( 1818) covalent geometry : angle 1.07113 ( 2436) hydrogen bonds : bond 0.20968 ( 16) hydrogen bonds : angle 10.80560 ( 48) Misc. bond : bond 0.01814 ( 12) link_BETA1-3 : bond 0.03647 ( 6) link_BETA1-3 : angle 1.31605 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.067 Fit side-chains REVERT: C 11 GLU cc_start: 0.7648 (tt0) cc_final: 0.7422 (tt0) REVERT: D 11 GLU cc_start: 0.7749 (tt0) cc_final: 0.7377 (tt0) REVERT: D 35 MET cc_start: 0.8973 (tpt) cc_final: 0.8732 (tpt) REVERT: B 28 LYS cc_start: 0.9201 (mttp) cc_final: 0.8952 (mttt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0814 time to fit residues: 3.1954 Evaluate side-chains 25 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN A 15 GLN B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.192590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140337 restraints weight = 1844.676| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.26 r_work: 0.3798 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 1836 Z= 0.123 Angle : 0.607 3.529 2454 Z= 0.301 Chirality : 0.053 0.131 312 Planarity : 0.002 0.006 288 Dihedral : 6.265 21.303 462 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.60 % Allowed : 14.88 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.46), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 10 PHE 0.013 0.003 PHE E 20 HIS 0.003 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 1818) covalent geometry : angle 0.59746 ( 2436) hydrogen bonds : bond 0.03636 ( 16) hydrogen bonds : angle 8.81885 ( 48) Misc. bond : bond 0.00093 ( 12) link_BETA1-3 : bond 0.00405 ( 6) link_BETA1-3 : angle 1.35727 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.057 Fit side-chains REVERT: D 11 GLU cc_start: 0.7506 (tt0) cc_final: 0.7266 (tt0) REVERT: D 35 MET cc_start: 0.9009 (tpt) cc_final: 0.8684 (tpt) REVERT: B 13 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6489 (m-70) REVERT: B 28 LYS cc_start: 0.9342 (mttp) cc_final: 0.9089 (mttt) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.0843 time to fit residues: 2.2959 Evaluate side-chains 24 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 HIS E 15 GLN F 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.194320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.141012 restraints weight = 1823.020| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.23 r_work: 0.3778 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1836 Z= 0.144 Angle : 0.566 3.936 2454 Z= 0.291 Chirality : 0.052 0.132 312 Planarity : 0.002 0.007 288 Dihedral : 4.875 16.250 462 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.60 % Allowed : 16.07 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.51), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.003 TYR B 10 PHE 0.013 0.003 PHE E 20 HIS 0.005 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 1818) covalent geometry : angle 0.55767 ( 2436) hydrogen bonds : bond 0.03068 ( 16) hydrogen bonds : angle 7.67673 ( 48) Misc. bond : bond 0.00064 ( 12) link_BETA1-3 : bond 0.00589 ( 6) link_BETA1-3 : angle 1.23864 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.075 Fit side-chains REVERT: D 11 GLU cc_start: 0.7833 (tt0) cc_final: 0.7507 (tt0) REVERT: B 13 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7390 (m-70) REVERT: B 16 LYS cc_start: 0.8536 (tttt) cc_final: 0.8260 (ttpt) REVERT: B 28 LYS cc_start: 0.9411 (mttp) cc_final: 0.9162 (mttt) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1044 time to fit residues: 2.7762 Evaluate side-chains 25 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4458 r_free = 0.4458 target = 0.190829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.138457 restraints weight = 1807.808| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.17 r_work: 0.3788 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1836 Z= 0.184 Angle : 0.592 3.871 2454 Z= 0.308 Chirality : 0.052 0.132 312 Planarity : 0.002 0.007 288 Dihedral : 4.485 16.012 462 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 2.38 % Allowed : 19.05 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.53), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.003 TYR B 10 PHE 0.015 0.003 PHE E 20 HIS 0.003 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 1818) covalent geometry : angle 0.58328 ( 2436) hydrogen bonds : bond 0.02924 ( 16) hydrogen bonds : angle 7.35618 ( 48) Misc. bond : bond 0.00054 ( 12) link_BETA1-3 : bond 0.00522 ( 6) link_BETA1-3 : angle 1.29429 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.066 Fit side-chains REVERT: B 13 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7368 (m-70) outliers start: 4 outliers final: 0 residues processed: 26 average time/residue: 0.0927 time to fit residues: 2.6801 Evaluate side-chains 24 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4456 r_free = 0.4456 target = 0.189394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.136473 restraints weight = 1824.126| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.23 r_work: 0.3785 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 1836 Z= 0.219 Angle : 0.619 4.911 2454 Z= 0.322 Chirality : 0.052 0.133 312 Planarity : 0.002 0.007 288 Dihedral : 4.293 16.216 462 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 2.98 % Allowed : 20.24 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.54), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.003 TYR D 10 PHE 0.016 0.003 PHE E 20 HIS 0.004 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 1818) covalent geometry : angle 0.61204 ( 2436) hydrogen bonds : bond 0.02963 ( 16) hydrogen bonds : angle 7.30783 ( 48) Misc. bond : bond 0.00041 ( 12) link_BETA1-3 : bond 0.00584 ( 6) link_BETA1-3 : angle 1.21034 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.052 Fit side-chains REVERT: B 13 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.7303 (m-70) outliers start: 5 outliers final: 0 residues processed: 25 average time/residue: 0.0898 time to fit residues: 2.5151 Evaluate side-chains 22 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.192967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.140101 restraints weight = 1814.360| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 3.22 r_work: 0.3831 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1836 Z= 0.133 Angle : 0.548 5.853 2454 Z= 0.278 Chirality : 0.050 0.132 312 Planarity : 0.002 0.006 288 Dihedral : 3.884 15.980 462 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.60 % Allowed : 23.21 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.55), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR F 10 PHE 0.013 0.002 PHE F 20 HIS 0.002 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 1818) covalent geometry : angle 0.54107 ( 2436) hydrogen bonds : bond 0.02127 ( 16) hydrogen bonds : angle 6.90812 ( 48) Misc. bond : bond 0.00039 ( 12) link_BETA1-3 : bond 0.00512 ( 6) link_BETA1-3 : angle 1.12041 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.065 Fit side-chains REVERT: B 13 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.7304 (m-70) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0948 time to fit residues: 2.3279 Evaluate side-chains 23 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 0.0070 chunk 5 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.198958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.146976 restraints weight = 1809.830| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 3.14 r_work: 0.3897 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1836 Z= 0.080 Angle : 0.485 4.616 2454 Z= 0.246 Chirality : 0.051 0.133 312 Planarity : 0.001 0.004 288 Dihedral : 3.538 15.373 462 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.19 % Allowed : 22.62 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.56), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR D 10 PHE 0.009 0.002 PHE F 20 HIS 0.002 0.000 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 1818) covalent geometry : angle 0.47656 ( 2436) hydrogen bonds : bond 0.01305 ( 16) hydrogen bonds : angle 6.18543 ( 48) Misc. bond : bond 0.00042 ( 12) link_BETA1-3 : bond 0.00439 ( 6) link_BETA1-3 : angle 1.12956 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.069 Fit side-chains REVERT: E 13 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.7220 (m-70) REVERT: D 11 GLU cc_start: 0.7808 (tt0) cc_final: 0.7505 (tt0) REVERT: B 13 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.7280 (m-70) outliers start: 2 outliers final: 0 residues processed: 23 average time/residue: 0.0868 time to fit residues: 2.2219 Evaluate side-chains 24 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain B residue 13 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- 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 = 0.4504 r_free = 0.4504 target = 0.194634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.141566 restraints weight = 1827.804| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.24 r_work: 0.3847 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1836 Z= 0.134 Angle : 0.538 5.285 2454 Z= 0.273 Chirality : 0.050 0.133 312 Planarity : 0.002 0.005 288 Dihedral : 3.552 14.450 462 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 0.60 % Allowed : 23.81 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 10 PHE 0.012 0.002 PHE E 20 HIS 0.002 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 1818) covalent geometry : angle 0.53071 ( 2436) hydrogen bonds : bond 0.01759 ( 16) hydrogen bonds : angle 6.14967 ( 48) Misc. bond : bond 0.00040 ( 12) link_BETA1-3 : bond 0.00479 ( 6) link_BETA1-3 : angle 1.15374 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.068 Fit side-chains REVERT: B 13 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7312 (m-70) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0972 time to fit residues: 2.3973 Evaluate side-chains 23 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.4463 r_free = 0.4463 target = 0.189386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.136256 restraints weight = 1826.780| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.25 r_work: 0.3786 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 1836 Z= 0.223 Angle : 0.622 6.348 2454 Z= 0.319 Chirality : 0.051 0.130 312 Planarity : 0.002 0.007 288 Dihedral : 3.902 15.784 462 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR D 10 PHE 0.016 0.003 PHE E 20 HIS 0.004 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 1818) covalent geometry : angle 0.61675 ( 2436) hydrogen bonds : bond 0.02514 ( 16) hydrogen bonds : angle 6.51072 ( 48) Misc. bond : bond 0.00038 ( 12) link_BETA1-3 : bond 0.00564 ( 6) link_BETA1-3 : angle 1.15497 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0873 time to fit residues: 2.2519 Evaluate side-chains 22 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.192666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.139584 restraints weight = 1837.992| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.26 r_work: 0.3825 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1836 Z= 0.147 Angle : 0.551 6.438 2454 Z= 0.282 Chirality : 0.051 0.135 312 Planarity : 0.002 0.006 288 Dihedral : 3.719 15.959 462 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 10 PHE 0.014 0.003 PHE F 20 HIS 0.003 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 1818) covalent geometry : angle 0.54560 ( 2436) hydrogen bonds : bond 0.01938 ( 16) hydrogen bonds : angle 6.36552 ( 48) Misc. bond : bond 0.00032 ( 12) link_BETA1-3 : bond 0.00483 ( 6) link_BETA1-3 : angle 1.08540 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0899 time to fit residues: 2.0226 Evaluate side-chains 20 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4515 r_free = 0.4515 target = 0.194989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.142300 restraints weight = 1839.110| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 3.18 r_work: 0.3858 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.003 0.014 1836 Z= 0.120 Angle : 0.521 6.116 2454 Z= 0.266 Chirality : 0.051 0.134 312 Planarity : 0.002 0.005 288 Dihedral : 3.559 15.349 462 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 0.00 % Allowed : 25.60 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.58), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR D 10 PHE 0.012 0.002 PHE E 20 HIS 0.002 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 1818) covalent geometry : angle 0.51428 ( 2436) hydrogen bonds : bond 0.01621 ( 16) hydrogen bonds : angle 6.08169 ( 48) Misc. bond : bond 0.00032 ( 12) link_BETA1-3 : bond 0.00458 ( 6) link_BETA1-3 : angle 1.11746 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 743.33 seconds wall clock time: 13 minutes 18.30 seconds (798.30 seconds total)