Starting phenix.real_space_refine on Wed Jul 23 10:03:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yl7_33903/07_2025/7yl7_33903.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yl7_33903/07_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_33903/07_2025/7yl7_33903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yl7_33903/07_2025/7yl7_33903.map" model { file = "/net/cci-nas-00/data/ceres_data/7yl7_33903/07_2025/7yl7_33903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yl7_33903/07_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-5711/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: 3.25, per 1000 atoms: 1.09 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: 0.98 Conformation dependent library (CDL) restraints added in 334.4 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: 0.32 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: 0.59 Time building geometry restraints manager: 0.97 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.140 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13800 ( 29) hydrogen bonds : angle 8.07466 ( 87) SS BOND : bond 0.00227 ( 6) SS BOND : angle 0.47448 ( 12) covalent geometry : bond 0.00948 ( 3024) covalent geometry : angle 0.87051 ( 4110) *********************** 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 : 0.319 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: 0.2225 time to fit residues: 9.0712 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 : 0.321 ------------------------------------------------------------------------------- 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: 0.3642 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 3030 Z= 0.199 Angle : 0.536 4.803 4122 Z= 0.295 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 Details of bonding type rmsd hydrogen bonds : bond 0.02381 ( 29) hydrogen bonds : angle 4.43386 ( 87) SS BOND : bond 0.00353 ( 6) SS BOND : angle 1.24749 ( 12) covalent geometry : bond 0.00405 ( 3024) covalent geometry : angle 0.53214 ( 4110) *********************** 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 : 0.344 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.8222 (mt) cc_final: 0.7966 (mt) REVERT: A 35 ASN cc_start: 0.8181 (m110) cc_final: 0.7960 (m110) REVERT: B 11 ARG cc_start: 0.7034 (mtt180) cc_final: 0.6339 (mmp-170) REVERT: I 11 ARG cc_start: 0.6906 (mtt180) cc_final: 0.5978 (mmp-170) outliers start: 9 outliers final: 5 residues processed: 31 average time/residue: 0.2049 time to fit residues: 7.6793 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 : 0.374 ------------------------------------------------------------------------------- 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: 0.8980 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.096684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.075466 restraints weight = 6710.251| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 3.10 r_work: 0.3854 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 3030 Z= 0.358 Angle : 0.664 5.775 4122 Z= 0.364 Chirality : 0.046 0.150 498 Planarity : 0.004 0.028 540 Dihedral : 13.542 50.783 486 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 3.09 % Allowed : 13.89 % 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 0.017 0.004 PHE G 15 ARG 0.004 0.001 ARG G 11 Details of bonding type rmsd hydrogen bonds : bond 0.01782 ( 29) hydrogen bonds : angle 3.99680 ( 87) SS BOND : bond 0.00306 ( 6) SS BOND : angle 0.55298 ( 12) covalent geometry : bond 0.00715 ( 3024) covalent geometry : angle 0.66423 ( 4110) *********************** 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: 10 poor density : 20 time to evaluate : 0.349 Fit side-chains REVERT: B 11 ARG cc_start: 0.6889 (mtt180) cc_final: 0.6558 (mmp-170) REVERT: L 34 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8120 (m) outliers start: 10 outliers final: 7 residues processed: 25 average time/residue: 0.1687 time to fit residues: 5.3332 Evaluate side-chains 25 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 34 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 0.0170 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.3422 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.098901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.076959 restraints weight = 6636.881| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.23 r_work: 0.3706 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3030 Z= 0.169 Angle : 0.515 4.722 4122 Z= 0.280 Chirality : 0.042 0.145 498 Planarity : 0.002 0.012 540 Dihedral : 10.452 41.766 486 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % 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 (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: -5.18 (0.25), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.19), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 18 PHE 0.008 0.002 PHE F 15 ARG 0.002 0.000 ARG G 11 Details of bonding type rmsd hydrogen bonds : bond 0.01364 ( 29) hydrogen bonds : angle 3.77417 ( 87) SS BOND : bond 0.00302 ( 6) SS BOND : angle 0.87903 ( 12) covalent geometry : bond 0.00334 ( 3024) covalent geometry : angle 0.51361 ( 4110) *********************** 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 31 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.359 Fit side-chains REVERT: A 22 ASN cc_start: 0.8272 (t0) cc_final: 0.7921 (t0) REVERT: B 11 ARG cc_start: 0.6892 (mtt180) cc_final: 0.6506 (mmp-170) REVERT: K 11 ARG cc_start: 0.6041 (mtt-85) cc_final: 0.5704 (pmt-80) REVERT: L 34 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8093 (m) outliers start: 6 outliers final: 4 residues processed: 28 average time/residue: 0.1951 time to fit residues: 6.6429 Evaluate side-chains 28 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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: 8.9990 chunk 2 optimal weight: 0.0670 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.097768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.075725 restraints weight = 6640.109| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.20 r_work: 0.3680 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3030 Z= 0.193 Angle : 0.523 6.071 4122 Z= 0.281 Chirality : 0.042 0.142 498 Planarity : 0.002 0.011 540 Dihedral : 9.073 31.956 486 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.47 % Allowed : 18.21 % 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: -5.20 (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 0.003 0.001 HIS E 18 PHE 0.009 0.002 PHE F 15 ARG 0.002 0.000 ARG G 11 Details of bonding type rmsd hydrogen bonds : bond 0.01179 ( 29) hydrogen bonds : angle 3.65068 ( 87) SS BOND : bond 0.00296 ( 6) SS BOND : angle 0.68588 ( 12) covalent geometry : bond 0.00385 ( 3024) covalent geometry : angle 0.52225 ( 4110) *********************** 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 34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.417 Fit side-chains REVERT: B 11 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6531 (mmp-170) REVERT: K 11 ARG cc_start: 0.5754 (mtt-85) cc_final: 0.5543 (pmt-80) REVERT: L 34 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.8125 (m) outliers start: 8 outliers final: 6 residues processed: 29 average time/residue: 0.1833 time to fit residues: 6.6783 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 : 0.349 ------------------------------------------------------------------------------- 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 11 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 29 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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** ** 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 = 0.4178 r_free = 0.4178 target = 0.096935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.075104 restraints weight = 6778.231| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.17 r_work: 0.3672 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3122 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= 0.234 Angle : 0.544 5.419 4122 Z= 0.294 Chirality : 0.042 0.146 498 Planarity : 0.002 0.016 540 Dihedral : 9.703 36.900 486 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % 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: -5.22 (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 0.004 0.001 HIS E 18 PHE 0.012 0.002 PHE G 15 ARG 0.002 0.000 ARG G 11 Details of bonding type rmsd hydrogen bonds : bond 0.01135 ( 29) hydrogen bonds : angle 3.71998 ( 87) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.64889 ( 12) covalent geometry : bond 0.00468 ( 3024) covalent geometry : angle 0.54409 ( 4110) *********************** 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: 7 poor density : 28 time to evaluate : 0.348 Fit side-chains REVERT: B 11 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6546 (mmp-170) REVERT: K 11 ARG cc_start: 0.5791 (mtt-85) cc_final: 0.5476 (pmt-80) REVERT: L 34 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8037 (m) REVERT: E 27 LEU cc_start: 0.8298 (tt) cc_final: 0.7844 (mp) REVERT: I 27 LEU cc_start: 0.7764 (tt) cc_final: 0.7297 (mp) outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.2084 time to fit residues: 7.4709 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 : 0.345 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 5 optimal weight: 0.0770 chunk 27 optimal weight: 30.0000 chunk 30 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 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 = 0.4258 r_free = 0.4258 target = 0.102435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.079653 restraints weight = 6351.389| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.29 r_work: 0.3952 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3030 Z= 0.079 Angle : 0.447 7.274 4122 Z= 0.232 Chirality : 0.040 0.135 498 Planarity : 0.001 0.006 540 Dihedral : 5.248 20.137 486 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: -5.19 (0.26), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.20), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 18 PHE 0.005 0.001 PHE K 15 ARG 0.001 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.00989 ( 29) hydrogen bonds : angle 3.50427 ( 87) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.95298 ( 12) covalent geometry : bond 0.00160 ( 3024) covalent geometry : angle 0.44502 ( 4110) *********************** 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 42 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.349 Fit side-chains REVERT: A 6 THR cc_start: 0.5500 (m) cc_final: 0.5240 (p) REVERT: A 22 ASN cc_start: 0.8457 (t0) cc_final: 0.8174 (t0) REVERT: B 11 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6720 (mmp-170) REVERT: K 11 ARG cc_start: 0.5657 (mtt-85) cc_final: 0.5434 (pmt-80) REVERT: E 27 LEU cc_start: 0.8345 (tt) cc_final: 0.7886 (mp) REVERT: I 27 LEU cc_start: 0.7955 (tt) cc_final: 0.7571 (mp) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.1741 time to fit residues: 8.2125 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 : 0.345 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** L 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 = 0.4239 r_free = 0.4239 target = 0.100674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.078463 restraints weight = 6416.279| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.17 r_work: 0.3920 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3358 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= 0.103 Angle : 0.456 6.955 4122 Z= 0.235 Chirality : 0.040 0.136 498 Planarity : 0.001 0.006 540 Dihedral : 5.696 18.208 486 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.23 % Allowed : 19.44 % 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: -5.10 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 18 PHE 0.005 0.001 PHE E 15 ARG 0.001 0.000 ARG G 11 Details of bonding type rmsd hydrogen bonds : bond 0.00936 ( 29) hydrogen bonds : angle 3.31602 ( 87) SS BOND : bond 0.00237 ( 6) SS BOND : angle 0.74862 ( 12) covalent geometry : bond 0.00206 ( 3024) covalent geometry : angle 0.45473 ( 4110) *********************** 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 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.352 Fit side-chains REVERT: A 6 THR cc_start: 0.5146 (m) cc_final: 0.4927 (p) REVERT: A 22 ASN cc_start: 0.8501 (t0) cc_final: 0.8189 (t0) REVERT: B 11 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6627 (mmp-170) REVERT: K 11 ARG cc_start: 0.5698 (mtt-85) cc_final: 0.5393 (pmt-80) REVERT: E 27 LEU cc_start: 0.8395 (tt) cc_final: 0.7932 (mp) REVERT: I 27 LEU cc_start: 0.7909 (tt) cc_final: 0.7533 (mp) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.2039 time to fit residues: 7.9900 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** ** 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 = 0.4201 r_free = 0.4201 target = 0.098530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.076557 restraints weight = 6654.658| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.17 r_work: 0.3834 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3030 Z= 0.175 Angle : 0.501 6.474 4122 Z= 0.260 Chirality : 0.041 0.141 498 Planarity : 0.002 0.013 540 Dihedral : 7.580 25.461 486 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.54 % Allowed : 19.14 % 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 (0.28), 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 0.003 0.001 HIS E 18 PHE 0.009 0.002 PHE F 15 ARG 0.002 0.000 ARG G 11 Details of bonding type rmsd hydrogen bonds : bond 0.01049 ( 29) hydrogen bonds : angle 3.42554 ( 87) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.56681 ( 12) covalent geometry : bond 0.00351 ( 3024) covalent geometry : angle 0.50113 ( 4110) *********************** 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: 5 poor density : 31 time to evaluate : 0.355 Fit side-chains REVERT: F 27 LEU cc_start: 0.7857 (tt) cc_final: 0.7547 (mp) REVERT: B 11 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6619 (mmp-170) REVERT: K 11 ARG cc_start: 0.5737 (mtt-85) cc_final: 0.5411 (pmt-80) REVERT: E 27 LEU cc_start: 0.8359 (tt) cc_final: 0.7855 (mp) REVERT: I 27 LEU cc_start: 0.7809 (tt) cc_final: 0.7382 (mp) outliers start: 5 outliers final: 5 residues processed: 31 average time/residue: 0.2078 time to fit residues: 7.7378 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain J 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: 0.0470 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- 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** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.096176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.074654 restraints weight = 6734.882| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.06 r_work: 0.3796 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3030 Z= 0.271 Angle : 0.573 5.419 4122 Z= 0.303 Chirality : 0.043 0.150 498 Planarity : 0.003 0.019 540 Dihedral : 10.129 39.825 486 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: -5.15 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 18 PHE 0.015 0.003 PHE G 15 ARG 0.003 0.000 ARG G 11 Details of bonding type rmsd hydrogen bonds : bond 0.01114 ( 29) hydrogen bonds : angle 3.67083 ( 87) SS BOND : bond 0.00279 ( 6) SS BOND : angle 0.45229 ( 12) covalent geometry : bond 0.00547 ( 3024) covalent geometry : angle 0.57290 ( 4110) ********************** 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 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.366 Fit side-chains REVERT: F 27 LEU cc_start: 0.8074 (tt) cc_final: 0.7723 (mp) REVERT: B 11 ARG cc_start: 0.7250 (mtt180) cc_final: 0.6609 (mmp-170) REVERT: K 11 ARG cc_start: 0.5420 (mtt-85) cc_final: 0.5152 (pmt-80) REVERT: K 34 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8217 (m) REVERT: E 27 LEU cc_start: 0.8386 (tt) cc_final: 0.7951 (mp) REVERT: I 27 LEU cc_start: 0.8061 (tt) cc_final: 0.7675 (mp) outliers start: 6 outliers final: 5 residues processed: 30 average time/residue: 0.2104 time to fit residues: 7.5659 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 : 0.320 ------------------------------------------------------------------------------- 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 H residue 26 ILE Chi-restraints excluded: chain J 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: 0.0030 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.0040 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- 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** ** L 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 = 0.4248 r_free = 0.4248 target = 0.101501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.079597 restraints weight = 6377.590| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.19 r_work: 0.3947 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 3030 Z= 0.076 Angle : 0.492 8.158 4122 Z= 0.236 Chirality : 0.041 0.137 498 Planarity : 0.001 0.008 540 Dihedral : 5.421 19.835 486 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.54 % Allowed : 19.14 % 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: -5.12 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 18 PHE 0.005 0.001 PHE L 15 ARG 0.001 0.000 ARG K 11 Details of bonding type rmsd hydrogen bonds : bond 0.00891 ( 29) hydrogen bonds : angle 3.44371 ( 87) SS BOND : bond 0.00194 ( 6) SS BOND : angle 0.84399 ( 12) covalent geometry : bond 0.00151 ( 3024) covalent geometry : angle 0.49041 ( 4110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.15 seconds wall clock time: 36 minutes 59.02 seconds (2219.02 seconds total)