Starting phenix.real_space_refine on Tue Mar 3 12:50:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rl4_24514/03_2026/7rl4_24514.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rl4_24514/03_2026/7rl4_24514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rl4_24514/03_2026/7rl4_24514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rl4_24514/03_2026/7rl4_24514.map" model { file = "/net/cci-nas-00/data/ceres_data/7rl4_24514/03_2026/7rl4_24514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rl4_24514/03_2026/7rl4_24514.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 2920 2.51 5 N 860 2.21 5 O 760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4620 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "K" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "G" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "L" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "Q" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "D" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "H" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "M" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "R" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "I" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "N" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "S" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "F" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "J" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "O" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "T" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Time building chain proxies: 1.26, per 1000 atoms: 0.27 Number of scatterers: 4620 At special positions: 0 Unit cell: (91.908, 85.284, 47.196, 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 80 16.00 O 760 8.00 N 860 7.00 C 2920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 189.6 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 109 through 112 removed outlier: 6.433A pdb=" N LYS C 110 " --> pdb=" O HIS D 111 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS A 110 " --> pdb=" O HIS E 111 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS E 110 " --> pdb=" O HIS F 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.446A pdb=" N MET A 134 " --> pdb=" O SER D 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 138 through 140 removed outlier: 6.458A pdb=" N ILE C 139 " --> pdb=" O HIS D 140 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 139 " --> pdb=" O HIS E 140 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE E 139 " --> pdb=" O HIS F 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 109 through 112 removed outlier: 6.412A pdb=" N LYS G 110 " --> pdb=" O HIS H 111 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 110 " --> pdb=" O HIS I 111 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS I 110 " --> pdb=" O HIS J 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 133 through 135 removed outlier: 6.381A pdb=" N MET B 134 " --> pdb=" O SER H 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 138 through 140 removed outlier: 6.339A pdb=" N ILE G 139 " --> pdb=" O HIS H 140 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE B 139 " --> pdb=" O HIS I 140 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE I 139 " --> pdb=" O HIS J 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 109 through 112 removed outlier: 6.474A pdb=" N LYS L 110 " --> pdb=" O HIS M 111 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS K 110 " --> pdb=" O HIS N 111 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS N 110 " --> pdb=" O HIS O 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 133 through 135 removed outlier: 6.399A pdb=" N MET K 134 " --> pdb=" O SER M 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 138 through 140 removed outlier: 6.491A pdb=" N ILE L 139 " --> pdb=" O HIS M 140 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE K 139 " --> pdb=" O HIS N 140 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE N 139 " --> pdb=" O HIS O 140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 109 through 112 removed outlier: 6.364A pdb=" N LYS Q 110 " --> pdb=" O HIS R 111 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS P 110 " --> pdb=" O HIS S 111 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS S 110 " --> pdb=" O HIS T 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 133 through 135 removed outlier: 6.425A pdb=" N MET P 134 " --> pdb=" O SER R 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 138 through 140 removed outlier: 6.298A pdb=" N ILE Q 139 " --> pdb=" O HIS R 140 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE P 139 " --> pdb=" O HIS S 140 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE S 139 " --> pdb=" O HIS T 140 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 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: 0.68 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1510 1.33 - 1.45: 694 1.45 - 1.56: 2336 1.56 - 1.68: 0 1.68 - 1.79: 160 Bond restraints: 4700 Sorted by residual: bond pdb=" CB VAL T 122 " pdb=" CG1 VAL T 122 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.46e+00 bond pdb=" CB VAL L 122 " pdb=" CG1 VAL L 122 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.40e+00 bond pdb=" CB VAL I 122 " pdb=" CG1 VAL I 122 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.39e+00 bond pdb=" CB VAL F 122 " pdb=" CG1 VAL F 122 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.38e+00 bond pdb=" CB VAL P 122 " pdb=" CG1 VAL P 122 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.36e+00 ... (remaining 4695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 4767 1.06 - 2.12: 992 2.12 - 3.18: 297 3.18 - 4.24: 162 4.24 - 5.30: 42 Bond angle restraints: 6260 Sorted by residual: angle pdb=" C ALA N 133 " pdb=" N MET N 134 " pdb=" CA MET N 134 " ideal model delta sigma weight residual 123.05 118.97 4.08 1.40e+00 5.10e-01 8.48e+00 angle pdb=" C ALA O 133 " pdb=" N MET O 134 " pdb=" CA MET O 134 " ideal model delta sigma weight residual 123.05 118.97 4.08 1.40e+00 5.10e-01 8.48e+00 angle pdb=" C ALA M 133 " pdb=" N MET M 134 " pdb=" CA MET M 134 " ideal model delta sigma weight residual 123.05 118.98 4.07 1.40e+00 5.10e-01 8.47e+00 angle pdb=" C ALA K 133 " pdb=" N MET K 134 " pdb=" CA MET K 134 " ideal model delta sigma weight residual 123.05 118.99 4.06 1.40e+00 5.10e-01 8.43e+00 angle pdb=" C ALA Q 133 " pdb=" N MET Q 134 " pdb=" CA MET Q 134 " ideal model delta sigma weight residual 123.05 118.99 4.06 1.40e+00 5.10e-01 8.39e+00 ... (remaining 6255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.17: 2132 11.17 - 22.33: 288 22.33 - 33.49: 160 33.49 - 44.66: 80 44.66 - 55.82: 20 Dihedral angle restraints: 2680 sinusoidal: 920 harmonic: 1760 Sorted by residual: dihedral pdb=" CA GLY N 131 " pdb=" C GLY N 131 " pdb=" N SER N 132 " pdb=" CA SER N 132 " ideal model delta harmonic sigma weight residual -180.00 -163.23 -16.77 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLY K 131 " pdb=" C GLY K 131 " pdb=" N SER K 132 " pdb=" CA SER K 132 " ideal model delta harmonic sigma weight residual -180.00 -163.25 -16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLY M 131 " pdb=" C GLY M 131 " pdb=" N SER M 132 " pdb=" CA SER M 132 " ideal model delta harmonic sigma weight residual -180.00 -163.25 -16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 2677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 338 0.046 - 0.092: 262 0.092 - 0.137: 13 0.137 - 0.183: 27 0.183 - 0.229: 20 Chirality restraints: 660 Sorted by residual: chirality pdb=" CB VAL S 122 " pdb=" CA VAL S 122 " pdb=" CG1 VAL S 122 " pdb=" CG2 VAL S 122 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL T 122 " pdb=" CA VAL T 122 " pdb=" CG1 VAL T 122 " pdb=" CG2 VAL T 122 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL R 122 " pdb=" CA VAL R 122 " pdb=" CG1 VAL R 122 " pdb=" CG2 VAL R 122 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 657 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 122 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C VAL E 122 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL E 122 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY E 123 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 122 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" C VAL F 122 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL F 122 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY F 123 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 122 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C VAL A 122 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 122 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 123 " -0.011 2.00e-02 2.50e+03 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 2677 3.01 - 3.48: 4029 3.48 - 3.95: 6890 3.95 - 4.43: 8976 4.43 - 4.90: 15493 Nonbonded interactions: 38065 Sorted by model distance: nonbonded pdb=" OG SER I 132 " pdb=" O LEU T 130 " model vdw 2.535 3.040 nonbonded pdb=" OG SER B 132 " pdb=" O LEU S 130 " model vdw 2.535 3.040 nonbonded pdb=" O LEU P 130 " pdb=" OG SER H 132 " model vdw 2.535 3.040 nonbonded pdb=" OG SER G 132 " pdb=" O LEU R 130 " model vdw 2.535 3.040 nonbonded pdb=" OG SER S 132 " pdb=" O LEU J 130 " model vdw 2.536 3.040 ... (remaining 38060 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'K' selection = chain 'P' selection = chain 'C' selection = chain 'G' selection = chain 'L' selection = chain 'Q' selection = chain 'D' selection = chain 'H' selection = chain 'M' selection = chain 'R' selection = chain 'E' selection = chain 'I' selection = chain 'N' selection = chain 'S' selection = chain 'F' selection = chain 'J' selection = chain 'O' selection = chain 'T' } 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: 1.870 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.620 Find NCS groups from input model: 0.050 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:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.015 0.077 4700 Z= 0.705 Angle : 1.156 5.297 6260 Z= 0.657 Chirality : 0.071 0.229 660 Planarity : 0.006 0.019 800 Dihedral : 16.037 55.821 1600 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.23), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.17), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.002 ARG D 136 TYR 0.014 0.004 TYR T 128 PHE 0.004 0.002 PHE J 141 HIS 0.013 0.005 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.01461 ( 4700) covalent geometry : angle 1.15588 ( 6260) hydrogen bonds : bond 0.10032 ( 44) hydrogen bonds : angle 9.05647 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7878 (mt) cc_final: 0.7380 (tp) REVERT: A 140 HIS cc_start: 0.7495 (m90) cc_final: 0.7171 (m-70) REVERT: K 138 ILE cc_start: 0.7850 (mt) cc_final: 0.7347 (tp) REVERT: K 140 HIS cc_start: 0.7439 (m90) cc_final: 0.7114 (m-70) REVERT: D 140 HIS cc_start: 0.7536 (m90) cc_final: 0.6997 (m-70) REVERT: M 140 HIS cc_start: 0.7455 (m90) cc_final: 0.7218 (m-70) REVERT: R 111 HIS cc_start: 0.7682 (t70) cc_final: 0.6992 (t-90) REVERT: E 129 MET cc_start: 0.8946 (ttt) cc_final: 0.8734 (ttp) REVERT: E 140 HIS cc_start: 0.7654 (m90) cc_final: 0.7243 (m-70) REVERT: I 111 HIS cc_start: 0.7757 (t70) cc_final: 0.7173 (t-90) REVERT: N 129 MET cc_start: 0.9039 (ttt) cc_final: 0.8834 (ttp) REVERT: N 140 HIS cc_start: 0.7591 (m90) cc_final: 0.7135 (m-70) REVERT: S 109 MET cc_start: 0.7507 (mtm) cc_final: 0.7286 (ttm) REVERT: S 111 HIS cc_start: 0.7777 (t70) cc_final: 0.7189 (t-90) REVERT: F 138 ILE cc_start: 0.7962 (mt) cc_final: 0.7519 (tp) REVERT: F 140 HIS cc_start: 0.7432 (m90) cc_final: 0.7036 (m-70) REVERT: J 111 HIS cc_start: 0.7580 (t70) cc_final: 0.7081 (t70) REVERT: O 138 ILE cc_start: 0.7925 (mt) cc_final: 0.7411 (tp) REVERT: O 140 HIS cc_start: 0.7483 (m90) cc_final: 0.7079 (m-70) outliers start: 0 outliers final: 1 residues processed: 183 average time/residue: 0.5068 time to fit residues: 96.1397 Evaluate side-chains 162 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 108 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.232577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.151932 restraints weight = 3527.058| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.43 r_work: 0.4016 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3927 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4700 Z= 0.162 Angle : 0.585 6.125 6260 Z= 0.295 Chirality : 0.045 0.118 660 Planarity : 0.003 0.025 800 Dihedral : 4.389 17.097 702 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 10.00 % Allowed : 22.00 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.56 (0.22), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.17), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.011 0.002 TYR O 128 PHE 0.004 0.001 PHE K 141 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4700) covalent geometry : angle 0.58488 ( 6260) hydrogen bonds : bond 0.00953 ( 44) hydrogen bonds : angle 5.61542 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7311 (ttm) cc_final: 0.6928 (pmm) REVERT: A 140 HIS cc_start: 0.7291 (m90) cc_final: 0.6933 (m-70) REVERT: K 134 MET cc_start: 0.7281 (ttm) cc_final: 0.6960 (pmm) REVERT: K 140 HIS cc_start: 0.7272 (m90) cc_final: 0.6914 (m-70) REVERT: L 138 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6444 (pp) REVERT: D 140 HIS cc_start: 0.7474 (m90) cc_final: 0.6894 (m-70) REVERT: H 111 HIS cc_start: 0.7809 (t70) cc_final: 0.7112 (t-90) REVERT: M 140 HIS cc_start: 0.7360 (m90) cc_final: 0.6777 (m-70) REVERT: R 111 HIS cc_start: 0.7786 (t70) cc_final: 0.6996 (t-90) REVERT: E 134 MET cc_start: 0.7359 (ttm) cc_final: 0.6891 (pmm) REVERT: E 140 HIS cc_start: 0.7555 (m90) cc_final: 0.7188 (m-70) REVERT: I 111 HIS cc_start: 0.7717 (t70) cc_final: 0.7116 (t-90) REVERT: I 136 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7646 (mtm180) REVERT: N 134 MET cc_start: 0.7401 (ttm) cc_final: 0.6934 (pmm) REVERT: N 140 HIS cc_start: 0.7560 (m90) cc_final: 0.7205 (m-70) REVERT: S 111 HIS cc_start: 0.7717 (t70) cc_final: 0.7068 (t-90) REVERT: S 136 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7594 (mtm180) REVERT: F 138 ILE cc_start: 0.7709 (mt) cc_final: 0.7139 (tp) REVERT: F 140 HIS cc_start: 0.7171 (m90) cc_final: 0.6632 (m-70) REVERT: J 111 HIS cc_start: 0.7656 (t70) cc_final: 0.7023 (t70) REVERT: J 136 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7601 (mtm180) REVERT: O 138 ILE cc_start: 0.7629 (mt) cc_final: 0.6987 (tp) REVERT: O 140 HIS cc_start: 0.7205 (m90) cc_final: 0.6686 (m-70) outliers start: 40 outliers final: 9 residues processed: 184 average time/residue: 0.4626 time to fit residues: 88.4909 Evaluate side-chains 187 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 129 MET Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain T residue 109 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 chunk 48 optimal weight: 0.0770 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.239359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.160974 restraints weight = 3528.699| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.46 r_work: 0.4102 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4017 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4700 Z= 0.110 Angle : 0.530 5.972 6260 Z= 0.259 Chirality : 0.045 0.121 660 Planarity : 0.003 0.030 800 Dihedral : 3.687 14.848 700 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.25 % Allowed : 26.25 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 136 TYR 0.009 0.001 TYR L 128 PHE 0.003 0.001 PHE I 141 HIS 0.002 0.001 HIS K 111 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4700) covalent geometry : angle 0.52980 ( 6260) hydrogen bonds : bond 0.01336 ( 44) hydrogen bonds : angle 5.19625 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 HIS cc_start: 0.7224 (m90) cc_final: 0.6886 (m-70) REVERT: K 134 MET cc_start: 0.7117 (ttm) cc_final: 0.6873 (pmm) REVERT: K 140 HIS cc_start: 0.7291 (m90) cc_final: 0.6957 (m-70) REVERT: P 111 HIS cc_start: 0.7741 (t70) cc_final: 0.7513 (t-90) REVERT: C 138 ILE cc_start: 0.6453 (OUTLIER) cc_final: 0.5866 (tp) REVERT: C 140 HIS cc_start: 0.7663 (m-70) cc_final: 0.7270 (m-70) REVERT: G 136 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7628 (mtm180) REVERT: D 140 HIS cc_start: 0.7354 (m90) cc_final: 0.6773 (m-70) REVERT: H 111 HIS cc_start: 0.7864 (t70) cc_final: 0.7178 (t-90) REVERT: M 140 HIS cc_start: 0.7318 (m90) cc_final: 0.6718 (m-70) REVERT: E 138 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.6847 (tp) REVERT: E 140 HIS cc_start: 0.7541 (m90) cc_final: 0.7154 (m-70) REVERT: I 136 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7588 (mtm180) REVERT: N 140 HIS cc_start: 0.7566 (m90) cc_final: 0.7192 (m-70) REVERT: S 136 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7636 (mtm180) REVERT: F 109 MET cc_start: 0.7348 (tpt) cc_final: 0.6550 (tpt) REVERT: F 112 MET cc_start: 0.8646 (ttt) cc_final: 0.8353 (ttt) REVERT: F 140 HIS cc_start: 0.7254 (m90) cc_final: 0.6732 (m-70) REVERT: J 136 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7575 (mtm180) REVERT: O 140 HIS cc_start: 0.7313 (m90) cc_final: 0.6837 (m-70) REVERT: T 122 VAL cc_start: 0.6764 (p) cc_final: 0.6478 (t) REVERT: T 136 ARG cc_start: 0.8068 (ttp-110) cc_final: 0.7417 (mtt180) outliers start: 33 outliers final: 9 residues processed: 185 average time/residue: 0.4743 time to fit residues: 91.2862 Evaluate side-chains 192 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain R residue 129 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain T residue 109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.0870 chunk 57 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 111 HIS S 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.212143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.133728 restraints weight = 3699.407| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.36 r_work: 0.3874 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 4700 Z= 0.391 Angle : 0.744 6.721 6260 Z= 0.369 Chirality : 0.047 0.111 660 Planarity : 0.005 0.040 800 Dihedral : 4.890 18.301 700 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 9.50 % Allowed : 33.00 % Favored : 57.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 136 TYR 0.017 0.003 TYR B 128 PHE 0.011 0.002 PHE S 141 HIS 0.006 0.002 HIS F 111 Details of bonding type rmsd covalent geometry : bond 0.00911 ( 4700) covalent geometry : angle 0.74412 ( 6260) hydrogen bonds : bond 0.01967 ( 44) hydrogen bonds : angle 5.13821 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8494 (mt) REVERT: P 125 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8427 (mp) REVERT: C 138 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6349 (tp) REVERT: C 140 HIS cc_start: 0.7703 (m-70) cc_final: 0.7321 (m-70) REVERT: L 138 ILE cc_start: 0.6683 (OUTLIER) cc_final: 0.6266 (tp) REVERT: L 140 HIS cc_start: 0.7456 (m90) cc_final: 0.7051 (m-70) REVERT: D 140 HIS cc_start: 0.7360 (m90) cc_final: 0.6681 (m-70) REVERT: H 111 HIS cc_start: 0.7861 (t70) cc_final: 0.7156 (t-90) REVERT: M 140 HIS cc_start: 0.7333 (m90) cc_final: 0.6647 (m-70) REVERT: E 129 MET cc_start: 0.8696 (ttm) cc_final: 0.8420 (ttt) REVERT: E 138 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.6922 (tp) REVERT: E 140 HIS cc_start: 0.7518 (m90) cc_final: 0.7069 (m-70) REVERT: I 109 MET cc_start: 0.7536 (mtm) cc_final: 0.7309 (ttm) REVERT: N 140 HIS cc_start: 0.7555 (m90) cc_final: 0.7126 (m-70) REVERT: S 109 MET cc_start: 0.7594 (mtm) cc_final: 0.7367 (ttm) REVERT: F 140 HIS cc_start: 0.7216 (m90) cc_final: 0.6665 (m-70) REVERT: O 140 HIS cc_start: 0.7160 (m90) cc_final: 0.6586 (m90) outliers start: 38 outliers final: 14 residues processed: 198 average time/residue: 0.4737 time to fit residues: 97.5577 Evaluate side-chains 202 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 129 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain J residue 129 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.0770 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS K 140 HIS S 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.216982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.139921 restraints weight = 3641.260| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.37 r_work: 0.3906 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 4700 Z= 0.283 Angle : 0.686 7.294 6260 Z= 0.333 Chirality : 0.045 0.115 660 Planarity : 0.003 0.018 800 Dihedral : 4.587 19.063 700 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 8.75 % Allowed : 35.75 % Favored : 55.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.71 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG R 136 TYR 0.013 0.002 TYR B 128 PHE 0.006 0.001 PHE Q 141 HIS 0.003 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00675 ( 4700) covalent geometry : angle 0.68578 ( 6260) hydrogen bonds : bond 0.01705 ( 44) hydrogen bonds : angle 4.63990 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 HIS cc_start: 0.7284 (m-70) cc_final: 0.7048 (m90) REVERT: B 125 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8440 (mt) REVERT: K 138 ILE cc_start: 0.7629 (mt) cc_final: 0.7231 (pp) REVERT: K 140 HIS cc_start: 0.7261 (m-70) cc_final: 0.7049 (m90) REVERT: P 111 HIS cc_start: 0.7803 (t70) cc_final: 0.7569 (t-90) REVERT: P 125 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8435 (mt) REVERT: C 109 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.6507 (tmt) REVERT: C 138 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6252 (tp) REVERT: C 140 HIS cc_start: 0.7631 (m-70) cc_final: 0.7249 (m-70) REVERT: L 138 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.6029 (tp) REVERT: L 140 HIS cc_start: 0.7432 (m90) cc_final: 0.6988 (m-70) REVERT: D 140 HIS cc_start: 0.7345 (m90) cc_final: 0.6643 (m-70) REVERT: H 111 HIS cc_start: 0.7827 (t70) cc_final: 0.7107 (t-90) REVERT: M 140 HIS cc_start: 0.7345 (m90) cc_final: 0.6652 (m-70) REVERT: E 138 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.6908 (tp) REVERT: E 140 HIS cc_start: 0.7409 (m90) cc_final: 0.6953 (m-70) REVERT: I 109 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7273 (ttm) REVERT: N 140 HIS cc_start: 0.7507 (m90) cc_final: 0.7124 (m-70) REVERT: S 109 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7327 (ttm) REVERT: F 140 HIS cc_start: 0.7233 (m90) cc_final: 0.6661 (m-70) outliers start: 35 outliers final: 11 residues processed: 194 average time/residue: 0.4571 time to fit residues: 92.3177 Evaluate side-chains 206 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain O residue 130 LEU Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.225749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.149066 restraints weight = 3658.221| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.45 r_work: 0.3987 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4700 Z= 0.158 Angle : 0.609 7.168 6260 Z= 0.291 Chirality : 0.044 0.117 660 Planarity : 0.003 0.019 800 Dihedral : 3.983 18.233 700 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 8.25 % Allowed : 34.50 % Favored : 57.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.66 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 136 TYR 0.008 0.001 TYR D 128 PHE 0.002 0.001 PHE R 141 HIS 0.002 0.000 HIS P 140 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4700) covalent geometry : angle 0.60926 ( 6260) hydrogen bonds : bond 0.01371 ( 44) hydrogen bonds : angle 4.44658 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7531 (mt) cc_final: 0.7182 (pp) REVERT: A 140 HIS cc_start: 0.7206 (m-70) cc_final: 0.6993 (m90) REVERT: B 125 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8428 (mt) REVERT: K 138 ILE cc_start: 0.7560 (mt) cc_final: 0.7179 (pp) REVERT: K 140 HIS cc_start: 0.7211 (m-70) cc_final: 0.7000 (m90) REVERT: P 111 HIS cc_start: 0.7778 (t70) cc_final: 0.7496 (t-90) REVERT: P 125 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8408 (mt) REVERT: C 109 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.6633 (tmt) REVERT: C 138 ILE cc_start: 0.6544 (OUTLIER) cc_final: 0.6198 (tp) REVERT: L 138 ILE cc_start: 0.6315 (OUTLIER) cc_final: 0.5921 (tp) REVERT: L 140 HIS cc_start: 0.7327 (m90) cc_final: 0.6912 (m-70) REVERT: Q 111 HIS cc_start: 0.7731 (t70) cc_final: 0.7482 (t-90) REVERT: D 140 HIS cc_start: 0.7313 (m90) cc_final: 0.6561 (m-70) REVERT: M 134 MET cc_start: 0.6835 (ttm) cc_final: 0.6382 (mmm) REVERT: M 140 HIS cc_start: 0.7298 (m90) cc_final: 0.6574 (m-70) REVERT: E 138 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.6915 (tp) REVERT: E 140 HIS cc_start: 0.7414 (m90) cc_final: 0.6982 (m-70) REVERT: I 109 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7236 (ttm) REVERT: N 140 HIS cc_start: 0.7511 (m90) cc_final: 0.7169 (m-70) REVERT: S 109 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7316 (ttm) REVERT: F 140 HIS cc_start: 0.7211 (m90) cc_final: 0.6655 (m-70) REVERT: J 122 VAL cc_start: 0.7392 (p) cc_final: 0.7135 (t) REVERT: T 122 VAL cc_start: 0.7185 (p) cc_final: 0.6928 (t) outliers start: 33 outliers final: 8 residues processed: 198 average time/residue: 0.4620 time to fit residues: 95.2532 Evaluate side-chains 205 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain S residue 109 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS I 111 HIS S 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.215324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.138478 restraints weight = 3721.890| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.39 r_work: 0.3910 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 4700 Z= 0.296 Angle : 0.715 7.369 6260 Z= 0.343 Chirality : 0.044 0.116 660 Planarity : 0.004 0.035 800 Dihedral : 4.609 16.947 700 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 8.25 % Allowed : 32.75 % Favored : 59.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 136 TYR 0.013 0.003 TYR P 128 PHE 0.007 0.001 PHE Q 141 HIS 0.003 0.001 HIS J 140 Details of bonding type rmsd covalent geometry : bond 0.00703 ( 4700) covalent geometry : angle 0.71534 ( 6260) hydrogen bonds : bond 0.01847 ( 44) hydrogen bonds : angle 4.53876 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7591 (mt) cc_final: 0.7176 (pp) REVERT: A 140 HIS cc_start: 0.7234 (m-70) cc_final: 0.7014 (m90) REVERT: K 138 ILE cc_start: 0.7612 (mt) cc_final: 0.7230 (pp) REVERT: K 140 HIS cc_start: 0.7237 (m-70) cc_final: 0.7022 (m90) REVERT: P 111 HIS cc_start: 0.7834 (t70) cc_final: 0.7577 (t-90) REVERT: P 125 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8479 (mp) REVERT: C 109 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.6661 (tmt) REVERT: C 138 ILE cc_start: 0.6673 (OUTLIER) cc_final: 0.6340 (tp) REVERT: G 111 HIS cc_start: 0.7801 (t70) cc_final: 0.7478 (t-90) REVERT: L 138 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.5976 (tp) REVERT: L 140 HIS cc_start: 0.7426 (m90) cc_final: 0.6995 (m-70) REVERT: Q 111 HIS cc_start: 0.7735 (t70) cc_final: 0.7432 (t-90) REVERT: D 140 HIS cc_start: 0.7391 (m90) cc_final: 0.6625 (m-70) REVERT: M 134 MET cc_start: 0.6904 (ttm) cc_final: 0.6514 (mmm) REVERT: M 140 HIS cc_start: 0.7319 (m90) cc_final: 0.6628 (m-70) REVERT: E 140 HIS cc_start: 0.7417 (m90) cc_final: 0.6961 (m-70) REVERT: I 109 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7213 (ttm) REVERT: N 109 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.5071 (tmt) REVERT: N 140 HIS cc_start: 0.7495 (m90) cc_final: 0.7112 (m-70) REVERT: S 109 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7286 (ttm) REVERT: F 140 HIS cc_start: 0.7193 (m90) cc_final: 0.6547 (m90) REVERT: J 109 MET cc_start: 0.7809 (mtt) cc_final: 0.7517 (mtp) outliers start: 33 outliers final: 12 residues processed: 199 average time/residue: 0.4371 time to fit residues: 90.5761 Evaluate side-chains 212 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain T residue 109 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 50 optimal weight: 0.1980 chunk 7 optimal weight: 0.0170 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS S 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.221930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.146113 restraints weight = 3681.859| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.39 r_work: 0.3964 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 4700 Z= 0.189 Angle : 0.660 6.988 6260 Z= 0.312 Chirality : 0.044 0.121 660 Planarity : 0.003 0.038 800 Dihedral : 4.152 17.928 700 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 7.75 % Allowed : 33.75 % Favored : 58.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 136 TYR 0.011 0.002 TYR T 128 PHE 0.004 0.001 PHE Q 141 HIS 0.002 0.001 HIS J 140 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 4700) covalent geometry : angle 0.66007 ( 6260) hydrogen bonds : bond 0.01648 ( 44) hydrogen bonds : angle 4.38734 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7551 (mt) cc_final: 0.7186 (pp) REVERT: A 140 HIS cc_start: 0.7241 (m-70) cc_final: 0.7032 (m90) REVERT: K 138 ILE cc_start: 0.7584 (mt) cc_final: 0.7226 (pp) REVERT: K 140 HIS cc_start: 0.7206 (m-70) cc_final: 0.6994 (m90) REVERT: P 111 HIS cc_start: 0.7747 (t70) cc_final: 0.7482 (t-90) REVERT: P 125 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8410 (mt) REVERT: C 109 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6631 (tmt) REVERT: C 138 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.6138 (tp) REVERT: G 111 HIS cc_start: 0.7761 (t70) cc_final: 0.7429 (t-90) REVERT: L 140 HIS cc_start: 0.7341 (m90) cc_final: 0.7019 (m-70) REVERT: Q 111 HIS cc_start: 0.7700 (t70) cc_final: 0.7374 (t-90) REVERT: D 140 HIS cc_start: 0.7346 (m90) cc_final: 0.6598 (m170) REVERT: M 134 MET cc_start: 0.6906 (ttm) cc_final: 0.6496 (mmm) REVERT: M 140 HIS cc_start: 0.7345 (m90) cc_final: 0.6643 (m-70) REVERT: E 140 HIS cc_start: 0.7497 (m90) cc_final: 0.7089 (m-70) REVERT: I 109 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7253 (ttm) REVERT: N 109 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.5178 (tmt) REVERT: N 140 HIS cc_start: 0.7397 (m90) cc_final: 0.7038 (m-70) REVERT: S 109 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7272 (ttm) REVERT: F 138 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.6977 (tp) REVERT: F 140 HIS cc_start: 0.7219 (m90) cc_final: 0.6586 (m90) REVERT: J 122 VAL cc_start: 0.7461 (p) cc_final: 0.7177 (t) REVERT: T 122 VAL cc_start: 0.7481 (p) cc_final: 0.7255 (t) outliers start: 31 outliers final: 13 residues processed: 195 average time/residue: 0.4613 time to fit residues: 93.5932 Evaluate side-chains 210 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 125 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 134 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain T residue 109 MET Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.225130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.149209 restraints weight = 3631.418| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.42 r_work: 0.4001 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4700 Z= 0.144 Angle : 0.649 6.935 6260 Z= 0.302 Chirality : 0.045 0.119 660 Planarity : 0.004 0.048 800 Dihedral : 3.879 16.933 700 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.00 % Allowed : 34.75 % Favored : 59.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.63 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 136 TYR 0.011 0.002 TYR T 128 PHE 0.002 0.001 PHE Q 141 HIS 0.001 0.000 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4700) covalent geometry : angle 0.64895 ( 6260) hydrogen bonds : bond 0.01767 ( 44) hydrogen bonds : angle 4.25327 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7555 (mt) cc_final: 0.7193 (pp) REVERT: A 140 HIS cc_start: 0.7234 (m-70) cc_final: 0.7010 (m90) REVERT: B 136 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7853 (mtp-110) REVERT: K 138 ILE cc_start: 0.7580 (mt) cc_final: 0.7217 (pp) REVERT: K 140 HIS cc_start: 0.7201 (m-70) cc_final: 0.6994 (m90) REVERT: P 111 HIS cc_start: 0.7734 (t70) cc_final: 0.7442 (t-90) REVERT: C 109 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.6460 (tmt) REVERT: G 111 HIS cc_start: 0.7734 (t70) cc_final: 0.7400 (t-90) REVERT: L 140 HIS cc_start: 0.7324 (m90) cc_final: 0.7017 (m-70) REVERT: D 140 HIS cc_start: 0.7376 (m90) cc_final: 0.6598 (m-70) REVERT: H 136 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7598 (mtm180) REVERT: M 134 MET cc_start: 0.6861 (ttm) cc_final: 0.6544 (mmm) REVERT: M 140 HIS cc_start: 0.7365 (m90) cc_final: 0.6653 (m-70) REVERT: E 140 HIS cc_start: 0.7487 (m90) cc_final: 0.7086 (m-70) REVERT: I 109 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7312 (ttm) REVERT: N 109 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.5359 (tmt) REVERT: N 129 MET cc_start: 0.8991 (ttt) cc_final: 0.8579 (ttt) REVERT: N 140 HIS cc_start: 0.7435 (m90) cc_final: 0.7092 (m-70) REVERT: S 109 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7276 (ttm) REVERT: F 138 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.6969 (tp) REVERT: F 140 HIS cc_start: 0.7250 (m90) cc_final: 0.6619 (m90) REVERT: J 122 VAL cc_start: 0.6909 (p) cc_final: 0.6644 (t) REVERT: J 136 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7439 (mtt180) outliers start: 24 outliers final: 9 residues processed: 193 average time/residue: 0.4319 time to fit residues: 86.9133 Evaluate side-chains 202 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 134 MET Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain T residue 109 MET Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 47 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 0.0020 chunk 36 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS I 111 HIS S 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.215203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.138692 restraints weight = 3746.601| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.38 r_work: 0.3904 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 4700 Z= 0.318 Angle : 0.778 7.766 6260 Z= 0.368 Chirality : 0.045 0.121 660 Planarity : 0.005 0.048 800 Dihedral : 4.651 18.141 700 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.50 % Allowed : 36.25 % Favored : 59.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 136 TYR 0.014 0.003 TYR B 128 PHE 0.008 0.002 PHE R 141 HIS 0.004 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00742 ( 4700) covalent geometry : angle 0.77809 ( 6260) hydrogen bonds : bond 0.02314 ( 44) hydrogen bonds : angle 4.57290 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.5915 (tmt) REVERT: A 138 ILE cc_start: 0.7538 (mt) cc_final: 0.7178 (pp) REVERT: A 140 HIS cc_start: 0.7253 (m-70) cc_final: 0.7034 (m90) REVERT: K 140 HIS cc_start: 0.7261 (m-70) cc_final: 0.7043 (m90) REVERT: P 111 HIS cc_start: 0.7800 (t70) cc_final: 0.7528 (t-90) REVERT: C 109 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.6464 (tmt) REVERT: L 138 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6398 (pp) REVERT: L 140 HIS cc_start: 0.7439 (m90) cc_final: 0.6982 (m-70) REVERT: D 140 HIS cc_start: 0.7393 (m90) cc_final: 0.6647 (m-70) REVERT: M 134 MET cc_start: 0.6850 (ttm) cc_final: 0.6629 (mmm) REVERT: M 138 ILE cc_start: 0.7807 (mt) cc_final: 0.7483 (pp) REVERT: M 140 HIS cc_start: 0.7370 (m90) cc_final: 0.6725 (m-70) REVERT: E 140 HIS cc_start: 0.7450 (m90) cc_final: 0.7066 (m-70) REVERT: I 109 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7291 (ttm) REVERT: N 109 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.5185 (tmt) REVERT: N 129 MET cc_start: 0.8974 (ttt) cc_final: 0.8624 (ttt) REVERT: N 140 HIS cc_start: 0.7410 (m90) cc_final: 0.7014 (m-70) REVERT: S 109 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7235 (ttm) REVERT: F 109 MET cc_start: 0.7556 (tpt) cc_final: 0.7046 (tpt) REVERT: F 138 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7081 (tp) REVERT: F 140 HIS cc_start: 0.7186 (m90) cc_final: 0.6909 (m-70) REVERT: J 109 MET cc_start: 0.7762 (mtt) cc_final: 0.7456 (mtp) outliers start: 18 outliers final: 6 residues processed: 197 average time/residue: 0.4464 time to fit residues: 91.7140 Evaluate side-chains 205 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 134 MET Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain J residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 35 optimal weight: 0.0570 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 111 HIS S 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.219100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.143036 restraints weight = 3689.212| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.39 r_work: 0.3961 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 4700 Z= 0.224 Angle : 0.732 8.007 6260 Z= 0.341 Chirality : 0.044 0.125 660 Planarity : 0.004 0.049 800 Dihedral : 4.345 17.241 700 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.50 % Allowed : 36.75 % Favored : 57.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 136 TYR 0.013 0.002 TYR E 128 PHE 0.004 0.001 PHE G 141 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 4700) covalent geometry : angle 0.73170 ( 6260) hydrogen bonds : bond 0.02059 ( 44) hydrogen bonds : angle 4.51535 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2461.43 seconds wall clock time: 42 minutes 28.87 seconds (2548.87 seconds total)