Starting phenix.real_space_refine on Fri Aug 22 13:04:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yl7_33903/08_2025/7yl7_33903.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yl7_33903/08_2025/7yl7_33903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yl7_33903/08_2025/7yl7_33903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yl7_33903/08_2025/7yl7_33903.map" model { file = "/net/cci-nas-00/data/ceres_data/7yl7_33903/08_2025/7yl7_33903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yl7_33903/08_2025/7yl7_33903.cif" } resolution = 3.3 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= 0.002 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 12 5.16 5 C 1818 2.51 5 N 558 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2988 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "B" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "K" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "G" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "L" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "H" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "J" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "I" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 0.95, per 1000 atoms: 0.32 Number of scatterers: 2988 At special positions: 0 Unit cell: (144.56, 84.24, 42.64, 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 12 16.00 O 600 8.00 N 558 7.00 C 1818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS A 2 " - pdb=" SG CYS A 7 " distance=2.03 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS J 2 " - pdb=" SG CYS J 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS I 2 " - pdb=" SG CYS I 7 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 115.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.541A pdb=" N THR F 9 " --> pdb=" O GLN A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19 removed outlier: 6.355A pdb=" N PHE F 15 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS A 18 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL F 17 " --> pdb=" O HIS A 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 31 through 32 removed outlier: 5.883A pdb=" N ASN F 31 " --> pdb=" O VAL A 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 9 through 22 removed outlier: 6.230A pdb=" N THR C 9 " --> pdb=" O GLN G 10 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU G 12 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG C 11 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ASN G 14 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA C 13 " --> pdb=" O ASN G 14 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LEU G 16 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE C 15 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N HIS G 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL C 17 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER G 20 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER C 19 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ASN G 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN C 21 " --> pdb=" O ASN G 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 26 through 28 removed outlier: 6.073A pdb=" N ILE K 26 " --> pdb=" O LEU G 27 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 22 removed outlier: 6.822A pdb=" N GLN L 10 " --> pdb=" O ARG H 11 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ALA H 13 " --> pdb=" O GLN L 10 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU L 12 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE H 15 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASN L 14 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL H 17 " --> pdb=" O ASN L 14 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU L 16 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N SER H 19 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N HIS L 18 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASN H 21 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER L 20 " --> pdb=" O ASN H 21 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR D 9 " --> pdb=" O GLN H 10 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU H 12 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG D 11 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ASN H 14 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA D 13 " --> pdb=" O ASN H 14 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LEU H 16 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE D 15 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N HIS H 18 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL D 17 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N SER H 20 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER D 19 " --> pdb=" O SER H 20 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ASN H 22 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN D 21 " --> pdb=" O ASN H 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 26 through 28 removed outlier: 6.074A pdb=" N ILE L 26 " --> pdb=" O LEU H 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 9 through 10 removed outlier: 6.567A pdb=" N THR J 9 " --> pdb=" O GLN E 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 14 through 19 removed outlier: 6.356A pdb=" N PHE J 15 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS E 18 " --> pdb=" O PHE J 15 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL J 17 " --> pdb=" O HIS E 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 31 through 32 removed outlier: 5.883A pdb=" N ASN J 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 29 hydrogen bonds defined for protein. 87 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: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 481 1.31 - 1.43: 864 1.43 - 1.56: 1667 1.56 - 1.68: 0 1.68 - 1.81: 12 Bond restraints: 3024 Sorted by residual: bond pdb=" CA THR B 6 " pdb=" C THR B 6 " ideal model delta sigma weight residual 1.532 1.475 0.058 9.60e-03 1.09e+04 3.63e+01 bond pdb=" C TYC B 37 " pdb=" NXT TYC B 37 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C TYC I 37 " pdb=" NXT TYC I 37 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C TYC F 37 " pdb=" NXT TYC F 37 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C TYC J 37 " pdb=" NXT TYC J 37 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 3019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 3962 2.13 - 4.26: 129 4.26 - 6.39: 18 6.39 - 8.52: 0 8.52 - 10.65: 1 Bond angle restraints: 4110 Sorted by residual: angle pdb=" C THR B 6 " pdb=" CA THR B 6 " pdb=" CB THR B 6 " ideal model delta sigma weight residual 112.27 101.62 10.65 1.75e+00 3.27e-01 3.70e+01 angle pdb=" C THR B 6 " pdb=" N CYS B 7 " pdb=" CA CYS B 7 " ideal model delta sigma weight residual 123.23 117.31 5.92 1.54e+00 4.22e-01 1.48e+01 angle pdb=" C ALA B 5 " pdb=" N THR B 6 " pdb=" CA THR B 6 " ideal model delta sigma weight residual 122.93 117.56 5.37 1.51e+00 4.39e-01 1.27e+01 angle pdb=" C ASN F 3 " pdb=" N THR F 4 " pdb=" CA THR F 4 " ideal model delta sigma weight residual 122.17 116.80 5.37 1.54e+00 4.22e-01 1.21e+01 angle pdb=" N ASN F 3 " pdb=" CA ASN F 3 " pdb=" C ASN F 3 " ideal model delta sigma weight residual 112.89 117.03 -4.14 1.24e+00 6.50e-01 1.12e+01 ... (remaining 4105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.38: 1511 11.38 - 22.75: 186 22.75 - 34.12: 37 34.12 - 45.50: 48 45.50 - 56.87: 30 Dihedral angle restraints: 1812 sinusoidal: 666 harmonic: 1146 Sorted by residual: dihedral pdb=" CB CYS J 2 " pdb=" SG CYS J 2 " pdb=" SG CYS J 7 " pdb=" CB CYS J 7 " ideal model delta sinusoidal sigma weight residual 93.00 36.13 56.87 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" CB CYS F 2 " pdb=" SG CYS F 2 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual 93.00 37.37 55.63 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS E 2 " pdb=" SG CYS E 2 " pdb=" SG CYS E 7 " pdb=" CB CYS E 7 " ideal model delta sinusoidal sigma weight residual 93.00 38.99 54.01 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 1809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 312 0.026 - 0.052: 114 0.052 - 0.079: 26 0.079 - 0.105: 26 0.105 - 0.131: 20 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE I 26 " pdb=" N ILE I 26 " pdb=" C ILE I 26 " pdb=" CB ILE I 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 495 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 13 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C ALA L 13 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA L 13 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN L 14 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 5 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C ALA A 5 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA A 5 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A 6 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 5 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C ALA F 5 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA F 5 " 0.014 2.00e-02 2.50e+03 pdb=" N THR F 6 " 0.012 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 253 2.74 - 3.28: 2893 3.28 - 3.82: 4557 3.82 - 4.36: 5253 4.36 - 4.90: 10203 Nonbonded interactions: 23159 Sorted by model distance: nonbonded pdb=" OG1 THR B 6 " pdb=" NE ARG K 11 " model vdw 2.196 3.120 nonbonded pdb=" OD1 ASN K 35 " pdb=" OD1 ASN J 35 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASN G 35 " pdb=" OD1 ASN I 35 " model vdw 2.210 3.040 nonbonded pdb=" O LYS J 1 " pdb=" O CYS I 2 " model vdw 2.243 3.040 nonbonded pdb=" O LYS F 1 " pdb=" O CYS B 2 " model vdw 2.243 3.040 ... (remaining 23154 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.300 Find NCS groups from input model: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.009 0.111 3030 Z= 0.514 Angle : 0.870 10.649 4122 Z= 0.501 Chirality : 0.041 0.131 498 Planarity : 0.003 0.029 540 Dihedral : 14.874 48.315 1038 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.16 (0.24), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.18), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 11 PHE 0.009 0.002 PHE J 15 HIS 0.002 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00948 ( 3024) covalent geometry : angle 0.87051 ( 4110) SS BOND : bond 0.00227 ( 6) SS BOND : angle 0.47448 ( 12) hydrogen bonds : bond 0.13800 ( 29) hydrogen bonds : angle 8.07466 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.127 Fit side-chains REVERT: B 11 ARG cc_start: 0.6687 (mtt180) cc_final: 0.5959 (mmm160) REVERT: B 14 ASN cc_start: 0.7951 (m-40) cc_final: 0.7326 (p0) REVERT: H 11 ARG cc_start: 0.4620 (mtt-85) cc_final: 0.4376 (mtp180) REVERT: I 11 ARG cc_start: 0.6767 (mtt180) cc_final: 0.5973 (mmm160) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0936 time to fit residues: 3.7879 Evaluate side-chains 21 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.099574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.077277 restraints weight = 6542.848| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.22 r_work: 0.3712 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3030 Z= 0.218 Angle : 0.553 4.967 4122 Z= 0.304 Chirality : 0.042 0.133 498 Planarity : 0.003 0.029 540 Dihedral : 11.466 43.291 486 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.78 % Allowed : 8.95 % Favored : 88.27 % 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 aren not related in a simple way. whole: -5.09 (0.24), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.18), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 11 PHE 0.012 0.002 PHE C 15 HIS 0.003 0.001 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 3024) covalent geometry : angle 0.54991 ( 4110) SS BOND : bond 0.00348 ( 6) SS BOND : angle 1.21457 ( 12) hydrogen bonds : bond 0.02193 ( 29) hydrogen bonds : angle 4.33350 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.8257 (mt) cc_final: 0.8004 (mt) REVERT: B 11 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6326 (mmp-170) REVERT: G 26 ILE cc_start: 0.8385 (mt) cc_final: 0.8185 (mt) REVERT: I 11 ARG cc_start: 0.6902 (mtt180) cc_final: 0.5977 (mmp-170) outliers start: 9 outliers final: 6 residues processed: 29 average time/residue: 0.0857 time to fit residues: 2.9381 Evaluate side-chains 29 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 34 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.098471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.076092 restraints weight = 6536.473| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.29 r_work: 0.3682 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3030 Z= 0.180 Angle : 0.489 4.470 4122 Z= 0.270 Chirality : 0.041 0.136 498 Planarity : 0.002 0.014 540 Dihedral : 8.534 29.085 486 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.16 % Allowed : 13.89 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.16 (0.24), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.18), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 11 PHE 0.010 0.002 PHE J 15 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3024) covalent geometry : angle 0.48784 ( 4110) SS BOND : bond 0.00286 ( 6) SS BOND : angle 0.74997 ( 12) hydrogen bonds : bond 0.01727 ( 29) hydrogen bonds : angle 3.82687 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.068 Fit side-chains REVERT: A 26 ILE cc_start: 0.8056 (mt) cc_final: 0.7825 (mt) REVERT: B 11 ARG cc_start: 0.6823 (mtt180) cc_final: 0.6511 (mmp-170) REVERT: L 34 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7864 (m) outliers start: 7 outliers final: 5 residues processed: 27 average time/residue: 0.0685 time to fit residues: 2.2443 Evaluate side-chains 28 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 23 optimal weight: 0.2980 chunk 8 optimal weight: 0.0870 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.098353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.076134 restraints weight = 6558.362| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.22 r_work: 0.3688 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3030 Z= 0.190 Angle : 0.492 4.370 4122 Z= 0.271 Chirality : 0.041 0.140 498 Planarity : 0.002 0.014 540 Dihedral : 8.252 29.675 486 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.85 % Allowed : 17.28 % Favored : 80.86 % 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 aren not related in a simple way. whole: -5.13 (0.24), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.19), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 11 PHE 0.010 0.002 PHE F 15 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3024) covalent geometry : angle 0.49130 ( 4110) SS BOND : bond 0.00306 ( 6) SS BOND : angle 0.70555 ( 12) hydrogen bonds : bond 0.01371 ( 29) hydrogen bonds : angle 3.62162 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.8203 (mt) cc_final: 0.7973 (mt) REVERT: B 11 ARG cc_start: 0.6881 (mtt180) cc_final: 0.6524 (mmp-170) REVERT: L 34 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8148 (m) outliers start: 6 outliers final: 5 residues processed: 29 average time/residue: 0.0704 time to fit residues: 2.5154 Evaluate side-chains 29 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.098501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.076336 restraints weight = 6523.435| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.21 r_work: 0.3691 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3030 Z= 0.185 Angle : 0.478 4.159 4122 Z= 0.263 Chirality : 0.041 0.139 498 Planarity : 0.002 0.012 540 Dihedral : 7.843 28.432 486 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.16 % Allowed : 18.21 % Favored : 79.63 % 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 aren not related in a simple way. whole: -5.14 (0.25), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.19), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 11 PHE 0.009 0.002 PHE F 15 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 3024) covalent geometry : angle 0.47736 ( 4110) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.61282 ( 12) hydrogen bonds : bond 0.01250 ( 29) hydrogen bonds : angle 3.57714 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.069 Fit side-chains REVERT: A 26 ILE cc_start: 0.8093 (mt) cc_final: 0.7879 (mt) REVERT: B 11 ARG cc_start: 0.7003 (mtt180) cc_final: 0.6530 (mmp-170) REVERT: K 11 ARG cc_start: 0.6028 (mtt-85) cc_final: 0.5777 (pmt-80) REVERT: L 34 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8064 (m) outliers start: 7 outliers final: 6 residues processed: 29 average time/residue: 0.0748 time to fit residues: 2.5805 Evaluate side-chains 30 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.096069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.074272 restraints weight = 6778.960| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.16 r_work: 0.3652 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3030 Z= 0.270 Angle : 0.547 4.519 4122 Z= 0.301 Chirality : 0.043 0.146 498 Planarity : 0.003 0.018 540 Dihedral : 10.130 40.401 486 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.47 % Allowed : 18.83 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.18 (0.26), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.20), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 11 PHE 0.012 0.003 PHE J 15 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 3024) covalent geometry : angle 0.54741 ( 4110) SS BOND : bond 0.00290 ( 6) SS BOND : angle 0.48177 ( 12) hydrogen bonds : bond 0.01263 ( 29) hydrogen bonds : angle 3.71176 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.089 Fit side-chains REVERT: A 26 ILE cc_start: 0.8268 (mt) cc_final: 0.8063 (mt) REVERT: B 11 ARG cc_start: 0.7135 (mtt180) cc_final: 0.6540 (mmp-170) REVERT: K 11 ARG cc_start: 0.5810 (mtt-85) cc_final: 0.5536 (pmt-80) REVERT: L 34 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.8053 (m) REVERT: H 11 ARG cc_start: 0.5103 (mtt-85) cc_final: 0.3939 (mtp180) REVERT: E 27 LEU cc_start: 0.8264 (tt) cc_final: 0.7808 (mp) REVERT: I 27 LEU cc_start: 0.7847 (tt) cc_final: 0.7335 (mp) outliers start: 8 outliers final: 6 residues processed: 30 average time/residue: 0.0671 time to fit residues: 2.3574 Evaluate side-chains 31 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.096891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.075232 restraints weight = 6804.279| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.18 r_work: 0.3806 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3030 Z= 0.231 Angle : 0.521 4.615 4122 Z= 0.285 Chirality : 0.042 0.146 498 Planarity : 0.002 0.016 540 Dihedral : 9.425 38.059 486 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.47 % Allowed : 17.59 % Favored : 79.94 % 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 aren not related in a simple way. whole: -5.23 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.20), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 11 PHE 0.010 0.002 PHE F 15 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 3024) covalent geometry : angle 0.52056 ( 4110) SS BOND : bond 0.00274 ( 6) SS BOND : angle 0.58934 ( 12) hydrogen bonds : bond 0.01199 ( 29) hydrogen bonds : angle 3.70940 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.090 Fit side-chains REVERT: B 11 ARG cc_start: 0.7180 (mtt180) cc_final: 0.6577 (mmp-170) REVERT: K 11 ARG cc_start: 0.5750 (mtt-85) cc_final: 0.5448 (pmt-80) REVERT: K 34 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7711 (m) REVERT: L 34 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.7999 (m) REVERT: H 11 ARG cc_start: 0.4986 (mtt-85) cc_final: 0.3885 (mtp180) REVERT: E 27 LEU cc_start: 0.8368 (tt) cc_final: 0.7930 (mp) REVERT: I 27 LEU cc_start: 0.7911 (tt) cc_final: 0.7499 (mp) outliers start: 8 outliers final: 5 residues processed: 28 average time/residue: 0.0944 time to fit residues: 3.0987 Evaluate side-chains 31 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.097381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.075579 restraints weight = 6787.683| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.19 r_work: 0.3670 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3030 Z= 0.192 Angle : 0.496 4.486 4122 Z= 0.269 Chirality : 0.042 0.144 498 Planarity : 0.002 0.013 540 Dihedral : 8.574 33.348 486 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.16 % Allowed : 17.90 % Favored : 79.94 % 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 aren not related in a simple way. whole: -5.20 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 11 PHE 0.009 0.002 PHE F 15 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 3024) covalent geometry : angle 0.49513 ( 4110) SS BOND : bond 0.00274 ( 6) SS BOND : angle 0.64990 ( 12) hydrogen bonds : bond 0.01112 ( 29) hydrogen bonds : angle 3.63511 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.121 Fit side-chains REVERT: A 22 ASN cc_start: 0.8463 (t0) cc_final: 0.8069 (t0) REVERT: B 11 ARG cc_start: 0.7014 (mtt180) cc_final: 0.6531 (mmp-170) REVERT: K 11 ARG cc_start: 0.5720 (mtt-85) cc_final: 0.5418 (pmt-80) REVERT: K 34 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7696 (m) REVERT: L 34 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7998 (m) REVERT: H 11 ARG cc_start: 0.4673 (mtt-85) cc_final: 0.3523 (mtp180) REVERT: E 27 LEU cc_start: 0.8378 (tt) cc_final: 0.7846 (mp) REVERT: I 27 LEU cc_start: 0.7778 (tt) cc_final: 0.7402 (mp) outliers start: 7 outliers final: 5 residues processed: 30 average time/residue: 0.0889 time to fit residues: 3.1315 Evaluate side-chains 34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS D 18 HIS ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.100799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.077020 restraints weight = 6380.983| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.74 r_work: 0.3724 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 3030 Z= 0.460 Angle : 0.745 5.301 4122 Z= 0.407 Chirality : 0.050 0.188 498 Planarity : 0.005 0.034 540 Dihedral : 13.555 46.670 486 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 2.16 % Allowed : 19.44 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.50 (0.26), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.20), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 11 PHE 0.022 0.005 PHE G 15 HIS 0.008 0.003 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00932 ( 3024) covalent geometry : angle 0.74581 ( 4110) SS BOND : bond 0.00281 ( 6) SS BOND : angle 0.46703 ( 12) hydrogen bonds : bond 0.01454 ( 29) hydrogen bonds : angle 4.52597 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.067 Fit side-chains REVERT: K 34 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8315 (m) REVERT: E 27 LEU cc_start: 0.8579 (tt) cc_final: 0.8192 (mp) outliers start: 7 outliers final: 3 residues processed: 28 average time/residue: 0.0779 time to fit residues: 2.5676 Evaluate side-chains 28 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.098603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.076602 restraints weight = 6632.641| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 3.14 r_work: 0.3883 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3030 Z= 0.124 Angle : 0.545 7.590 4122 Z= 0.274 Chirality : 0.042 0.147 498 Planarity : 0.001 0.009 540 Dihedral : 8.438 30.455 486 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.23 % Allowed : 19.75 % Favored : 79.01 % 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 aren not related in a simple way. whole: -5.36 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 11 PHE 0.008 0.001 PHE L 15 HIS 0.002 0.000 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3024) covalent geometry : angle 0.54464 ( 4110) SS BOND : bond 0.00239 ( 6) SS BOND : angle 0.74285 ( 12) hydrogen bonds : bond 0.00985 ( 29) hydrogen bonds : angle 3.88393 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.110 Fit side-chains REVERT: A 22 ASN cc_start: 0.8535 (t0) cc_final: 0.8213 (t0) REVERT: B 27 LEU cc_start: 0.8059 (tt) cc_final: 0.7612 (mp) REVERT: K 34 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7949 (m) REVERT: E 27 LEU cc_start: 0.8510 (tt) cc_final: 0.8050 (mp) REVERT: I 27 LEU cc_start: 0.8146 (tt) cc_final: 0.7686 (mp) outliers start: 4 outliers final: 2 residues processed: 32 average time/residue: 0.0771 time to fit residues: 2.8996 Evaluate side-chains 33 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.094630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.073108 restraints weight = 6949.638| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.00 r_work: 0.3781 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3030 Z= 0.283 Angle : 0.633 8.018 4122 Z= 0.327 Chirality : 0.044 0.152 498 Planarity : 0.003 0.018 540 Dihedral : 10.659 41.231 486 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.23 % Allowed : 19.75 % Favored : 79.01 % 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 aren not related in a simple way. whole: -5.35 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 11 PHE 0.014 0.003 PHE G 15 HIS 0.005 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 3024) covalent geometry : angle 0.63372 ( 4110) SS BOND : bond 0.00289 ( 6) SS BOND : angle 0.53276 ( 12) hydrogen bonds : bond 0.01121 ( 29) hydrogen bonds : angle 4.22244 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 869.27 seconds wall clock time: 15 minutes 33.49 seconds (933.49 seconds total)