Starting phenix.real_space_refine on Mon Feb 10 19:49:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f29_31428/02_2025/7f29_31428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f29_31428/02_2025/7f29_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_31428/02_2025/7f29_31428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f29_31428/02_2025/7f29_31428.map" model { file = "/net/cci-nas-00/data/ceres_data/7f29_31428/02_2025/7f29_31428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f29_31428/02_2025/7f29_31428.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1794 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" 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: "A" 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, B, E, D, F, I, H, K, J, L Time building chain proxies: 1.54, per 1000 atoms: 0.86 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: 0.80 Conformation dependent library (CDL) restraints added in 212.8 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: 0.29 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: 0.37 Time building geometry restraints manager: 0.78 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 0.400 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: 0.020 Set scattering table: 0.020 Process input model: 9.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.760 ------------------------------------------------------------------------------- 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 1818 Z= 0.794 Angle : 1.071 6.744 2436 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.001 HIS E 14 PHE 0.014 0.003 PHE A 20 TYR 0.005 0.003 TYR E 10 *********************** 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 : 0.148 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: 0.1893 time to fit residues: 7.4173 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 : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.0040 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.4491 r_free = 0.4491 target = 0.194843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.143121 restraints weight = 1849.369| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.22 r_work: 0.3831 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1818 Z= 0.140 Angle : 0.572 3.314 2436 Z= 0.284 Chirality : 0.053 0.133 312 Planarity : 0.002 0.006 288 Dihedral : 5.873 18.659 462 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.46), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 13 PHE 0.011 0.002 PHE E 20 TYR 0.008 0.002 TYR D 10 *********************** 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 : 0.147 Fit side-chains REVERT: D 11 GLU cc_start: 0.7679 (tt0) cc_final: 0.7448 (tt0) REVERT: B 13 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.6542 (m-70) REVERT: B 28 LYS cc_start: 0.9383 (mttp) cc_final: 0.9135 (mttt) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1867 time to fit residues: 5.1095 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 : 0.196 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN F 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.199776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.146385 restraints weight = 1787.327| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 3.21 r_work: 0.3865 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1818 Z= 0.150 Angle : 0.514 3.516 2436 Z= 0.266 Chirality : 0.051 0.133 312 Planarity : 0.002 0.006 288 Dihedral : 4.685 15.492 462 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.60 % Allowed : 16.67 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.52), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 13 PHE 0.010 0.002 PHE E 20 TYR 0.009 0.003 TYR E 10 *********************** 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 22 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.218 Fit side-chains REVERT: D 11 GLU cc_start: 0.7757 (tt0) cc_final: 0.7487 (tt0) REVERT: B 13 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7313 (m-70) REVERT: B 16 LYS cc_start: 0.8549 (tttt) cc_final: 0.8308 (ttpt) REVERT: B 28 LYS cc_start: 0.9418 (mttp) cc_final: 0.9110 (mtmt) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.2673 time to fit residues: 6.3291 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 : 0.196 ------------------------------------------------------------------------------- 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 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.188990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.136288 restraints weight = 1847.651| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.25 r_work: 0.3766 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 1818 Z= 0.376 Angle : 0.638 4.598 2436 Z= 0.334 Chirality : 0.052 0.129 312 Planarity : 0.002 0.008 288 Dihedral : 4.608 16.104 462 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 2.98 % Allowed : 13.10 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.53), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 14 PHE 0.017 0.003 PHE F 20 TYR 0.007 0.003 TYR F 10 *********************** 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: 5 poor density : 20 time to evaluate : 0.180 Fit side-chains REVERT: A 34 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8805 (tt) REVERT: B 13 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7388 (m-70) outliers start: 5 outliers final: 0 residues processed: 24 average time/residue: 0.2271 time to fit residues: 6.0898 Evaluate side-chains 22 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU 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 11 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.0010 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 = 0.4522 r_free = 0.4522 target = 0.196435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.144057 restraints weight = 1791.417| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.19 r_work: 0.3870 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1818 Z= 0.140 Angle : 0.495 4.099 2436 Z= 0.256 Chirality : 0.050 0.134 312 Planarity : 0.001 0.006 288 Dihedral : 3.993 15.850 462 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 2.38 % Allowed : 16.67 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.54), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 14 PHE 0.011 0.002 PHE F 20 TYR 0.007 0.002 TYR B 10 *********************** 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 24 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.178 Fit side-chains REVERT: D 11 GLU cc_start: 0.7841 (tt0) cc_final: 0.7558 (tt0) REVERT: B 13 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.7336 (m-70) outliers start: 4 outliers final: 0 residues processed: 23 average time/residue: 0.2150 time to fit residues: 5.5717 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 : 0.177 ------------------------------------------------------------------------------- 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 15 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 7 optimal weight: 0.0370 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 HIS B 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.202144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.149857 restraints weight = 1802.122| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.19 r_work: 0.3919 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1818 Z= 0.116 Angle : 0.480 4.998 2436 Z= 0.243 Chirality : 0.051 0.132 312 Planarity : 0.001 0.005 288 Dihedral : 3.487 13.980 462 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.60 % Allowed : 19.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (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 HIS 0.001 0.000 HIS F 13 PHE 0.008 0.002 PHE E 20 TYR 0.007 0.002 TYR B 10 *********************** 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 20 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.197 Fit side-chains REVERT: D 11 GLU cc_start: 0.7779 (tt0) cc_final: 0.7509 (tt0) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.2303 time to fit residues: 5.1763 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 : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 0.0370 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 = 0.4556 r_free = 0.4556 target = 0.200821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148432 restraints weight = 1793.866| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.13 r_work: 0.3906 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1818 Z= 0.130 Angle : 0.481 4.148 2436 Z= 0.246 Chirality : 0.050 0.131 312 Planarity : 0.001 0.005 288 Dihedral : 3.465 14.115 462 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 20.24 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.009 0.002 PHE E 20 TYR 0.009 0.002 TYR B 10 *********************** 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 19 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.193 Fit side-chains REVERT: D 11 GLU cc_start: 0.7750 (tt0) cc_final: 0.7468 (tt0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2447 time to fit residues: 5.2233 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 : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 0.0030 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.202057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.149686 restraints weight = 1787.415| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 3.09 r_work: 0.3921 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1818 Z= 0.118 Angle : 0.463 4.626 2436 Z= 0.238 Chirality : 0.050 0.132 312 Planarity : 0.001 0.004 288 Dihedral : 3.333 13.731 462 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 22.02 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 14 PHE 0.008 0.002 PHE E 20 TYR 0.005 0.002 TYR B 10 *********************** 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 19 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.180 Fit side-chains REVERT: D 11 GLU cc_start: 0.7741 (tt0) cc_final: 0.7467 (tt0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2553 time to fit residues: 5.4269 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 : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.197870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.144159 restraints weight = 1800.409| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 3.24 r_work: 0.3862 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1818 Z= 0.182 Angle : 0.511 5.285 2436 Z= 0.262 Chirality : 0.050 0.132 312 Planarity : 0.001 0.005 288 Dihedral : 3.430 13.961 462 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 22.02 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.58), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.011 0.002 PHE F 20 TYR 0.010 0.002 TYR B 10 *********************** 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 : 0.292 Fit side-chains REVERT: D 11 GLU cc_start: 0.7650 (tt0) cc_final: 0.7346 (tt0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2506 time to fit residues: 5.3158 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 : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.192013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.138045 restraints weight = 1875.594| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.33 r_work: 0.3800 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 1818 Z= 0.315 Angle : 0.584 6.341 2436 Z= 0.303 Chirality : 0.051 0.133 312 Planarity : 0.002 0.007 288 Dihedral : 3.693 14.879 462 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 23.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.58), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 14 PHE 0.015 0.003 PHE F 20 TYR 0.008 0.003 TYR B 10 ********************** 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 22 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.185 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2242 time to fit residues: 5.5657 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 : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.197871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.144383 restraints weight = 1777.549| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 3.23 r_work: 0.3876 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1818 Z= 0.141 Angle : 0.481 5.537 2436 Z= 0.249 Chirality : 0.050 0.134 312 Planarity : 0.001 0.005 288 Dihedral : 3.472 15.301 462 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.00 % Allowed : 23.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.58), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.012 0.002 PHE F 20 TYR 0.009 0.002 TYR B 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1475.34 seconds wall clock time: 26 minutes 43.46 seconds (1603.46 seconds total)