Starting phenix.real_space_refine on Mon Feb 10 22:06:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yl7_33903/02_2025/7yl7_33903.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yl7_33903/02_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_33903/02_2025/7yl7_33903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yl7_33903/02_2025/7yl7_33903.map" model { file = "/net/cci-nas-00/data/ceres_data/7yl7_33903/02_2025/7yl7_33903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yl7_33903/02_2025/7yl7_33903.cif" } resolution = 3.3 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= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 2.35, per 1000 atoms: 0.79 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: 0.83 Conformation dependent library (CDL) restraints added in 364.8 milliseconds 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: 0.31 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: 0.57 Time building geometry restraints manager: 0.90 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: 0.800 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.650 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- 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 3024 Z= 0.674 Angle : 0.871 10.649 4110 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 (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: -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 HIS 0.002 0.001 HIS J 18 PHE 0.009 0.002 PHE J 15 ARG 0.002 0.001 ARG H 11 *********************** 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 : 0.309 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: 0.2358 time to fit residues: 9.5877 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 : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.100118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.077786 restraints weight = 6361.302| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.20 r_work: 0.3720 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3024 Z= 0.277 Angle : 0.532 4.803 4110 Z= 0.294 Chirality : 0.042 0.132 498 Planarity : 0.003 0.029 540 Dihedral : 11.108 41.145 486 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.78 % Allowed : 8.64 % Favored : 88.58 % 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: -5.11 (0.23), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.18), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 18 PHE 0.011 0.002 PHE C 15 ARG 0.002 0.000 ARG K 11 *********************** 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 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.8221 (mt) cc_final: 0.7965 (mt) REVERT: A 35 ASN cc_start: 0.8182 (m110) cc_final: 0.7962 (m110) REVERT: B 11 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6349 (mmp-170) REVERT: I 11 ARG cc_start: 0.6924 (mtt180) cc_final: 0.5995 (mmp-170) outliers start: 9 outliers final: 5 residues processed: 31 average time/residue: 0.1818 time to fit residues: 6.8493 Evaluate side-chains 30 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.0010 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 2.9592 ------------------------------------------------------------------------------- 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 18 HIS ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.095351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.073788 restraints weight = 6694.523| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.14 r_work: 0.3639 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 3024 Z= 0.463 Angle : 0.645 5.679 4110 Z= 0.354 Chirality : 0.046 0.145 498 Planarity : 0.003 0.027 540 Dihedral : 13.173 48.474 486 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.78 % Allowed : 14.20 % Favored : 83.02 % 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: -5.09 (0.25), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.19), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 18 PHE 0.016 0.004 PHE G 15 ARG 0.003 0.000 ARG G 11 *********************** 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 30 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.356 Fit side-chains REVERT: A 26 ILE cc_start: 0.8398 (mt) cc_final: 0.8187 (mt) REVERT: B 11 ARG cc_start: 0.6843 (mtt180) cc_final: 0.6530 (mmp-170) outliers start: 9 outliers final: 7 residues processed: 26 average time/residue: 0.1672 time to fit residues: 5.5473 Evaluate side-chains 26 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER 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 Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain I residue 34 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** ** L 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 = 0.4190 r_free = 0.4190 target = 0.097299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.075530 restraints weight = 6753.234| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.20 r_work: 0.3678 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3024 Z= 0.316 Angle : 0.559 5.243 4110 Z= 0.303 Chirality : 0.042 0.144 498 Planarity : 0.002 0.017 540 Dihedral : 11.530 46.089 486 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.85 % Allowed : 17.90 % Favored : 80.25 % 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: -5.19 (0.25), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.19), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 18 PHE 0.011 0.002 PHE C 15 ARG 0.002 0.000 ARG G 11 *********************** 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 29 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.343 Fit side-chains REVERT: A 26 ILE cc_start: 0.8319 (mt) cc_final: 0.8119 (mt) REVERT: A 35 ASN cc_start: 0.8252 (m110) cc_final: 0.7970 (m-40) REVERT: B 11 ARG cc_start: 0.6942 (mtt180) cc_final: 0.6518 (mmp-170) REVERT: K 11 ARG cc_start: 0.6145 (mtt-85) cc_final: 0.5739 (pmt-80) REVERT: L 34 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8110 (m) outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.1980 time to fit residues: 6.3622 Evaluate side-chains 26 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.4084 ------------------------------------------------------------------------------- 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** L 35 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.098441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.076457 restraints weight = 6614.458| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.18 r_work: 0.3695 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3024 Z= 0.237 Angle : 0.510 6.256 4110 Z= 0.272 Chirality : 0.041 0.140 498 Planarity : 0.002 0.011 540 Dihedral : 8.441 31.580 486 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % 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 (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: -5.22 (0.25), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.19), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 18 PHE 0.009 0.002 PHE F 15 ARG 0.002 0.000 ARG G 11 *********************** 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 38 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.360 Fit side-chains REVERT: A 26 ILE cc_start: 0.8289 (mt) cc_final: 0.8086 (mt) REVERT: B 11 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6545 (mmp-170) REVERT: K 11 ARG cc_start: 0.5770 (mtt-85) cc_final: 0.5525 (pmt-80) REVERT: L 34 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8057 (m) REVERT: H 11 ARG cc_start: 0.4969 (mtt-85) cc_final: 0.3930 (mtp180) REVERT: E 27 LEU cc_start: 0.8310 (tt) cc_final: 0.7796 (mp) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 0.1920 time to fit residues: 7.8211 Evaluate side-chains 34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4157 r_free = 0.4157 target = 0.095407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.073936 restraints weight = 6947.943| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.11 r_work: 0.3784 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3024 Z= 0.438 Angle : 0.616 5.136 4110 Z= 0.335 Chirality : 0.044 0.147 498 Planarity : 0.003 0.022 540 Dihedral : 11.465 44.904 486 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.47 % Allowed : 19.14 % 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 (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: -5.24 (0.26), 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 HIS 0.005 0.002 HIS E 18 PHE 0.017 0.003 PHE G 15 ARG 0.003 0.000 ARG G 11 *********************** 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 34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.315 Fit side-chains REVERT: F 27 LEU cc_start: 0.7966 (tt) cc_final: 0.7568 (mp) REVERT: A 26 ILE cc_start: 0.8406 (mt) cc_final: 0.8193 (mt) REVERT: B 11 ARG cc_start: 0.7116 (mtt180) cc_final: 0.6545 (mmp-170) REVERT: K 11 ARG cc_start: 0.5805 (mtt-85) cc_final: 0.5407 (pmt-80) REVERT: K 34 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7880 (m) REVERT: D 11 ARG cc_start: 0.4113 (mmt180) cc_final: 0.3777 (mmt180) REVERT: E 27 LEU cc_start: 0.8387 (tt) cc_final: 0.7944 (mp) REVERT: I 27 LEU cc_start: 0.8113 (tt) cc_final: 0.7666 (mp) outliers start: 8 outliers final: 6 residues processed: 30 average time/residue: 0.2073 time to fit residues: 7.4136 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 : 0.326 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 30.0000 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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** ** A 35 ASN ** 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 = 0.4244 r_free = 0.4244 target = 0.101199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.079140 restraints weight = 6448.676| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.27 r_work: 0.3937 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3024 Z= 0.115 Angle : 0.460 6.117 4110 Z= 0.241 Chirality : 0.041 0.142 498 Planarity : 0.001 0.007 540 Dihedral : 5.937 21.368 486 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.47 % Allowed : 19.14 % 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 (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: -5.22 (0.26), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.20), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 18 PHE 0.006 0.001 PHE G 15 ARG 0.001 0.000 ARG I 11 *********************** 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 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.348 Fit side-chains REVERT: B 11 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6684 (mmp-170) REVERT: K 11 ARG cc_start: 0.5722 (mtt-85) cc_final: 0.5407 (pmt-80) REVERT: K 34 SER cc_start: 0.7899 (OUTLIER) cc_final: 0.7584 (m) REVERT: G 34 SER cc_start: 0.8782 (t) cc_final: 0.8505 (p) REVERT: E 27 LEU cc_start: 0.8401 (tt) cc_final: 0.7901 (mp) REVERT: I 27 LEU cc_start: 0.7992 (tt) cc_final: 0.7554 (mp) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.2030 time to fit residues: 8.0206 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4230 r_free = 0.4230 target = 0.100073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.078038 restraints weight = 6470.597| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.19 r_work: 0.3911 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3024 Z= 0.150 Angle : 0.456 6.984 4110 Z= 0.239 Chirality : 0.040 0.140 498 Planarity : 0.001 0.006 540 Dihedral : 6.030 19.163 486 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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 (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: -5.12 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.20), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 18 PHE 0.006 0.001 PHE G 15 ARG 0.001 0.000 ARG G 11 *********************** 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 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.345 Fit side-chains REVERT: A 6 THR cc_start: 0.5168 (OUTLIER) cc_final: 0.4910 (p) REVERT: B 11 ARG cc_start: 0.7066 (mtt180) cc_final: 0.6610 (mmp-170) REVERT: K 11 ARG cc_start: 0.5713 (mtt-85) cc_final: 0.5418 (pmt-80) REVERT: E 27 LEU cc_start: 0.8430 (tt) cc_final: 0.7940 (mp) REVERT: I 27 LEU cc_start: 0.8006 (tt) cc_final: 0.7566 (mp) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.1915 time to fit residues: 7.6216 Evaluate side-chains 33 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4189 r_free = 0.4189 target = 0.097762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.075996 restraints weight = 6708.068| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.14 r_work: 0.3826 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3024 Z= 0.249 Angle : 0.497 6.401 4110 Z= 0.262 Chirality : 0.041 0.143 498 Planarity : 0.002 0.013 540 Dihedral : 7.763 26.550 486 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.16 % Allowed : 19.14 % 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 (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: -5.04 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 18 PHE 0.010 0.002 PHE G 15 ARG 0.002 0.000 ARG G 11 *********************** 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 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.350 Fit side-chains REVERT: F 27 LEU cc_start: 0.7859 (tt) cc_final: 0.7599 (mp) REVERT: B 11 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6608 (mmp-170) REVERT: B 27 LEU cc_start: 0.7810 (tt) cc_final: 0.7369 (mp) REVERT: K 11 ARG cc_start: 0.5671 (mtt-85) cc_final: 0.5355 (pmt-80) REVERT: K 34 SER cc_start: 0.8093 (OUTLIER) cc_final: 0.7680 (m) REVERT: E 27 LEU cc_start: 0.8379 (tt) cc_final: 0.7888 (mp) REVERT: I 27 LEU cc_start: 0.7863 (tt) cc_final: 0.7498 (mp) outliers start: 7 outliers final: 6 residues processed: 31 average time/residue: 0.2111 time to fit residues: 7.8089 Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 L residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain I residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 0.0670 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4219 r_free = 0.4219 target = 0.099540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.077659 restraints weight = 6488.076| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.16 r_work: 0.3901 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3024 Z= 0.165 Angle : 0.460 6.786 4110 Z= 0.238 Chirality : 0.040 0.140 498 Planarity : 0.001 0.008 540 Dihedral : 6.223 19.274 486 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.16 % Allowed : 18.83 % 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 (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: -5.01 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 18 PHE 0.006 0.001 PHE G 15 ARG 0.001 0.000 ARG G 11 ********************** 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 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.353 Fit side-chains REVERT: F 27 LEU cc_start: 0.8066 (tt) cc_final: 0.7737 (mp) REVERT: A 6 THR cc_start: 0.5229 (OUTLIER) cc_final: 0.4968 (p) REVERT: B 11 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6639 (mmp-170) REVERT: B 27 LEU cc_start: 0.7931 (tt) cc_final: 0.7490 (mp) REVERT: K 11 ARG cc_start: 0.5582 (mtt-85) cc_final: 0.5303 (pmt-80) REVERT: K 34 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7836 (m) REVERT: E 27 LEU cc_start: 0.8436 (tt) cc_final: 0.7981 (mp) REVERT: I 27 LEU cc_start: 0.8029 (tt) cc_final: 0.7685 (mp) outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.2041 time to fit residues: 7.8670 Evaluate side-chains 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 L residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain I residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.0270 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 0.0030 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.098222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.076336 restraints weight = 6631.376| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 3.17 r_work: 0.3868 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3024 Z= 0.232 Angle : 0.484 6.740 4110 Z= 0.252 Chirality : 0.041 0.142 498 Planarity : 0.002 0.012 540 Dihedral : 7.315 24.214 486 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.85 % Allowed : 18.83 % Favored : 79.32 % 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: -5.03 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 18 PHE 0.009 0.002 PHE G 15 ARG 0.002 0.000 ARG G 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.80 seconds wall clock time: 36 minutes 20.03 seconds (2180.03 seconds total)