Starting phenix.real_space_refine on Wed Jul 1 20:45:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f29_31428/07_2026/7f29_31428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f29_31428/07_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_31428/07_2026/7f29_31428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f29_31428/07_2026/7f29_31428.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7f29_31428/07_2026/7f29_31428.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f29_31428/07_2026/7f29_31428.cif" model { file = "/net/cci-nas-00/data/ceres_data/7f29_31428/07_2026/7f29_31428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f29_31428/07_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-6108/lib/python3.11/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 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: 0.54, per 1000 atoms: 0.30 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: 0.38 Conformation dependent library (CDL) restraints added in 68.0 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: 0.06 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: 0.32 Time building geometry restraints manager: 0.33 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: 840 16.94 - 33.88: 66 33.88 - 50.82: 6 50.82 - 67.76: 6 67.76 - 84.70: 6 Dihedral angle restraints: 924 sinusoidal: 336 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 921 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: 0.900 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.410 Find NCS groups from input model: 0.020 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 15.695 84.703 552 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/Z covalent geometry : bond 0.01381 / 0.68 ( 1818) covalent geometry : angle 1.07113 / 0.45 ( 2436) hydrogen bonds : bond 0.20968 / 16.38 ( 16) hydrogen bonds : angle 10.80560 / 7.38 ( 48) Misc. bond : bond 0.01814 / 1.67 ( 12) link_BETA1-3 : bond 0.03647 / 2.17 ( 6) link_BETA1-3 : angle 1.31605 / 0.99 ( 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 : 0.068 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: 0.0811 time to fit residues: 3.2032 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 : 0.067 ------------------------------------------------------------------------------- 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: 2.9990 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... 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 = 0.4470 r_free = 0.4470 target = 0.192498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.140368 restraints weight = 1843.860| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.22 r_work: 0.3793 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1187 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= 0.126 Angle : 0.631 3.749 2454 Z= 0.305 Chirality : 0.053 0.133 312 Planarity : 0.002 0.006 288 Dihedral : 4.966 16.510 216 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % 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: -3.27 (0.46), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 10 PHE 0.013 0.003 PHE E 20 HIS 0.002 0.001 HIS E 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 1818) covalent geometry : angle 0.62911 / 0.31 ( 2436) hydrogen bonds : bond 0.03441 / 2.62 ( 16) hydrogen bonds : angle 8.82743 / 6.07 ( 48) Misc. bond : bond 0.00079 / 0.05 ( 12) link_BETA1-3 : bond 0.00388 / 0.24 ( 6) link_BETA1-3 : angle 0.87416 / 0.67 ( 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 : 0.072 Fit side-chains REVERT: D 11 GLU cc_start: 0.7705 (tt0) cc_final: 0.7456 (tt0) REVERT: D 35 MET cc_start: 0.9047 (tpt) cc_final: 0.8717 (tpt) REVERT: B 13 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.6629 (m-70) REVERT: B 28 LYS cc_start: 0.9388 (mttp) cc_final: 0.9146 (mttt) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.0805 time to fit residues: 2.1969 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 : 0.069 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4443 r_free = 0.4443 target = 0.189728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.136747 restraints weight = 1861.315| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.27 r_work: 0.3759 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 1836 Z= 0.197 Angle : 0.646 3.755 2454 Z= 0.324 Chirality : 0.052 0.133 312 Planarity : 0.002 0.007 288 Dihedral : 4.973 16.056 216 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.60 % Allowed : 14.29 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.50), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.003 TYR F 10 PHE 0.015 0.003 PHE E 20 HIS 0.003 0.001 HIS B 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 1818) covalent geometry : angle 0.64281 / 0.32 ( 2436) hydrogen bonds : bond 0.03579 / 2.68 ( 16) hydrogen bonds : angle 8.15504 / 5.59 ( 48) Misc. bond : bond 0.00059 / 0.04 ( 12) link_BETA1-3 : bond 0.00546 / 0.33 ( 6) link_BETA1-3 : angle 0.99960 / 0.73 ( 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 24 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.067 Fit side-chains REVERT: B 13 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.7330 (m-70) REVERT: B 28 LYS cc_start: 0.9390 (mttp) cc_final: 0.9098 (mtmt) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.1075 time to fit residues: 2.7434 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 : 0.071 ------------------------------------------------------------------------------- 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: 9.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.192156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.138940 restraints weight = 1805.414| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.24 r_work: 0.3800 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1836 Z= 0.152 Angle : 0.574 3.379 2454 Z= 0.290 Chirality : 0.051 0.133 312 Planarity : 0.002 0.006 288 Dihedral : 4.902 16.083 216 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 2.38 % Allowed : 17.26 % Favored : 80.36 % 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: -2.56 (0.52), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.003 TYR F 10 PHE 0.013 0.002 PHE E 20 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 1818) covalent geometry : angle 0.57025 / 0.29 ( 2436) hydrogen bonds : bond 0.02506 / 1.88 ( 16) hydrogen bonds : angle 7.38673 / 5.11 ( 48) Misc. bond : bond 0.00053 / 0.03 ( 12) link_BETA1-3 : bond 0.00498 / 0.30 ( 6) link_BETA1-3 : angle 0.97393 / 0.71 ( 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 25 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.074 Fit side-chains REVERT: B 13 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7323 (m-70) outliers start: 4 outliers final: 0 residues processed: 24 average time/residue: 0.0940 time to fit residues: 2.5396 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 : 0.071 ------------------------------------------------------------------------------- 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: 4.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 0.0370 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.193261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.140991 restraints weight = 1794.392| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 3.17 r_work: 0.3825 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1845 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= 0.143 Angle : 0.570 4.187 2454 Z= 0.286 Chirality : 0.051 0.132 312 Planarity : 0.002 0.006 288 Dihedral : 4.774 15.565 216 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % 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: -2.37 (0.54), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 10 PHE 0.013 0.002 PHE E 20 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 1818) covalent geometry : angle 0.56564 / 0.29 ( 2436) hydrogen bonds : bond 0.02239 / 1.71 ( 16) hydrogen bonds : angle 7.03173 / 4.88 ( 48) Misc. bond : bond 0.00048 / 0.03 ( 12) link_BETA1-3 : bond 0.00525 / 0.31 ( 6) link_BETA1-3 : angle 1.00728 / 0.74 ( 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 : 0.070 Fit side-chains REVERT: B 13 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.7313 (m-70) outliers start: 5 outliers final: 0 residues processed: 25 average time/residue: 0.0892 time to fit residues: 2.5155 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 : 0.067 ------------------------------------------------------------------------------- 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: 4.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.196927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.144973 restraints weight = 1804.848| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.19 r_work: 0.3873 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1836 Z= 0.091 Angle : 0.525 4.311 2454 Z= 0.259 Chirality : 0.051 0.133 312 Planarity : 0.001 0.005 288 Dihedral : 4.577 15.709 216 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.60 % Allowed : 22.62 % 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: -2.21 (0.55), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR F 10 PHE 0.010 0.002 PHE F 20 HIS 0.002 0.000 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 ( 1818) covalent geometry : angle 0.51997 / 0.26 ( 2436) hydrogen bonds : bond 0.01580 / 1.21 ( 16) hydrogen bonds : angle 6.52136 / 4.57 ( 48) Misc. bond : bond 0.00046 / 0.03 ( 12) link_BETA1-3 : bond 0.00452 / 0.26 ( 6) link_BETA1-3 : angle 0.97637 / 0.73 ( 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 : 0.068 Fit side-chains REVERT: D 11 GLU cc_start: 0.7822 (tt0) cc_final: 0.7494 (tt0) REVERT: B 13 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.7256 (m-70) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0953 time to fit residues: 2.3380 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 ------------------------------------------------------------------------------- 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: 0.4980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.200515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.148059 restraints weight = 1803.372| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 3.15 r_work: 0.3902 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2354 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= 0.083 Angle : 0.497 3.780 2454 Z= 0.247 Chirality : 0.051 0.132 312 Planarity : 0.001 0.004 288 Dihedral : 4.290 14.766 216 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.60 % Allowed : 22.62 % 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: -2.02 (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 D 10 PHE 0.009 0.002 PHE F 20 HIS 0.002 0.001 HIS E 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.08 ( 1818) covalent geometry : angle 0.49027 / 0.25 ( 2436) hydrogen bonds : bond 0.01202 / 0.94 ( 16) hydrogen bonds : angle 5.77045 / 4.05 ( 48) Misc. bond : bond 0.00046 / 0.03 ( 12) link_BETA1-3 : bond 0.00438 / 0.26 ( 6) link_BETA1-3 : angle 1.04568 / 0.78 ( 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 22 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.045 Fit side-chains REVERT: D 11 GLU cc_start: 0.7781 (tt0) cc_final: 0.7452 (tt0) REVERT: B 13 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.7244 (m-70) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0845 time to fit residues: 1.9753 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 : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.201884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.148683 restraints weight = 1794.596| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.23 r_work: 0.3908 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2408 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= 0.083 Angle : 0.501 4.888 2454 Z= 0.247 Chirality : 0.051 0.132 312 Planarity : 0.001 0.005 288 Dihedral : 4.248 14.114 216 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -1.98 (0.58), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR F 10 PHE 0.009 0.002 PHE F 20 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.08 ( 1818) covalent geometry : angle 0.49421 / 0.25 ( 2436) hydrogen bonds : bond 0.01204 / 0.94 ( 16) hydrogen bonds : angle 5.54616 / 3.93 ( 48) Misc. bond : bond 0.00045 / 0.03 ( 12) link_BETA1-3 : bond 0.00439 / 0.26 ( 6) link_BETA1-3 : angle 1.05927 / 0.79 ( 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 20 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.068 Fit side-chains REVERT: D 11 GLU cc_start: 0.7596 (tt0) cc_final: 0.7272 (tt0) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.1145 time to fit residues: 2.5295 Evaluate side-chains 19 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.202071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.149226 restraints weight = 1771.978| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.18 r_work: 0.3917 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2474 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= 0.082 Angle : 0.488 5.250 2454 Z= 0.242 Chirality : 0.051 0.132 312 Planarity : 0.001 0.005 288 Dihedral : 4.138 13.444 216 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.00 % Allowed : 24.40 % 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: -1.89 (0.59), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR D 10 PHE 0.008 0.002 PHE F 20 HIS 0.001 0.001 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.08 ( 1818) covalent geometry : angle 0.48123 / 0.24 ( 2436) hydrogen bonds : bond 0.01052 / 0.83 ( 16) hydrogen bonds : angle 5.37799 / 3.81 ( 48) Misc. bond : bond 0.00042 / 0.02 ( 12) link_BETA1-3 : bond 0.00428 / 0.25 ( 6) link_BETA1-3 : angle 1.08201 / 0.81 ( 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 19 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.054 Fit side-chains REVERT: D 11 GLU cc_start: 0.7585 (tt0) cc_final: 0.7264 (tt0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0988 time to fit residues: 2.0967 Evaluate side-chains 19 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.065 ------------------------------------------------------------------------------- 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: 4.9990 chunk 16 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.201797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.148983 restraints weight = 1788.331| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.18 r_work: 0.3918 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2555 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= 0.084 Angle : 0.492 5.427 2454 Z= 0.244 Chirality : 0.050 0.132 312 Planarity : 0.001 0.005 288 Dihedral : 4.157 13.206 216 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.11 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: -1.86 (0.59), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 10 PHE 0.009 0.002 PHE F 20 HIS 0.002 0.000 HIS E 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.08 ( 1818) covalent geometry : angle 0.48452 / 0.24 ( 2436) hydrogen bonds : bond 0.01167 / 0.93 ( 16) hydrogen bonds : angle 5.32904 / 3.79 ( 48) Misc. bond : bond 0.00039 / 0.02 ( 12) link_BETA1-3 : bond 0.00421 / 0.25 ( 6) link_BETA1-3 : angle 1.10073 / 0.83 ( 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 19 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.064 Fit side-chains REVERT: D 11 GLU cc_start: 0.7586 (tt0) cc_final: 0.7264 (tt0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0998 time to fit residues: 2.1192 Evaluate side-chains 19 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.068 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.196614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.142879 restraints weight = 1828.819| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.27 r_work: 0.3854 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2437 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= 0.141 Angle : 0.547 5.963 2454 Z= 0.275 Chirality : 0.051 0.133 312 Planarity : 0.002 0.005 288 Dihedral : 4.379 13.853 216 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.11 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: -1.91 (0.59), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 10 PHE 0.012 0.003 PHE E 20 HIS 0.002 0.001 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 1818) covalent geometry : angle 0.54040 / 0.27 ( 2436) hydrogen bonds : bond 0.01683 / 1.35 ( 16) hydrogen bonds : angle 5.67522 / 3.99 ( 48) Misc. bond : bond 0.00043 / 0.02 ( 12) link_BETA1-3 : bond 0.00440 / 0.26 ( 6) link_BETA1-3 : angle 1.11903 / 0.84 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 748.03 seconds wall clock time: 13 minutes 29.02 seconds (809.02 seconds total)