Starting phenix.real_space_refine on Thu Mar 6 02:51:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rl4_24514/03_2025/7rl4_24514.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rl4_24514/03_2025/7rl4_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_2025/7rl4_24514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rl4_24514/03_2025/7rl4_24514.map" model { file = "/net/cci-nas-00/data/ceres_data/7rl4_24514/03_2025/7rl4_24514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rl4_24514/03_2025/7rl4_24514.cif" } resolution = 2.86 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 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.19, per 1000 atoms: 0.69 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: 1.04 Conformation dependent library (CDL) restraints added in 640.3 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: 0.71 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: 1.00 Time building geometry restraints manager: 1.25 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' 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: 0.690 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.430 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.790 ------------------------------------------------------------------------------- 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= 1.032 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 (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: -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 HIS 0.013 0.005 HIS I 111 PHE 0.004 0.002 PHE J 141 TYR 0.014 0.004 TYR T 128 ARG 0.004 0.002 ARG D 136 *********************** 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 : 0.464 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: 1.0902 time to fit residues: 207.0291 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 : 0.475 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4582 r_free = 0.4582 target = 0.234219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.153546 restraints weight = 3485.332| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.41 r_work: 0.4042 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4700 Z= 0.236 Angle : 0.581 6.205 6260 Z= 0.293 Chirality : 0.045 0.118 660 Planarity : 0.003 0.024 800 Dihedral : 4.384 17.233 702 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 9.75 % Allowed : 21.25 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.56 (0.22), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 111 PHE 0.004 0.001 PHE K 141 TYR 0.010 0.002 TYR O 128 ARG 0.005 0.001 ARG I 136 *********************** 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: 39 poor density : 185 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7333 (ttm) cc_final: 0.6923 (pmm) REVERT: A 140 HIS cc_start: 0.7320 (m90) cc_final: 0.6957 (m-70) REVERT: K 134 MET cc_start: 0.7329 (ttm) cc_final: 0.6928 (pmm) REVERT: K 140 HIS cc_start: 0.7311 (m90) cc_final: 0.6950 (m-70) REVERT: L 138 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6519 (pp) REVERT: D 140 HIS cc_start: 0.7489 (m90) cc_final: 0.6913 (m-70) REVERT: H 111 HIS cc_start: 0.7780 (t70) cc_final: 0.7081 (t-90) REVERT: M 140 HIS cc_start: 0.7367 (m90) cc_final: 0.6786 (m-70) REVERT: R 111 HIS cc_start: 0.7771 (t70) cc_final: 0.6968 (t-90) REVERT: E 134 MET cc_start: 0.7337 (ttm) cc_final: 0.6889 (pmm) REVERT: E 140 HIS cc_start: 0.7607 (m90) cc_final: 0.7242 (m-70) REVERT: I 111 HIS cc_start: 0.7717 (t70) cc_final: 0.7118 (t-90) REVERT: I 136 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7616 (mtm180) REVERT: N 134 MET cc_start: 0.7357 (ttm) cc_final: 0.6947 (pmm) REVERT: N 140 HIS cc_start: 0.7549 (m90) cc_final: 0.7188 (m-70) REVERT: S 111 HIS cc_start: 0.7719 (t70) cc_final: 0.7076 (t-90) REVERT: S 136 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7593 (mtm180) REVERT: F 138 ILE cc_start: 0.7697 (mt) cc_final: 0.7119 (tp) REVERT: F 140 HIS cc_start: 0.7223 (m90) cc_final: 0.6687 (m-70) REVERT: J 111 HIS cc_start: 0.7672 (t70) cc_final: 0.7034 (t70) REVERT: J 136 ARG cc_start: 0.8193 (ttp-110) cc_final: 0.7576 (mtm180) REVERT: O 138 ILE cc_start: 0.7651 (mt) cc_final: 0.6996 (tp) REVERT: O 140 HIS cc_start: 0.7259 (m90) cc_final: 0.6748 (m-70) outliers start: 39 outliers final: 7 residues processed: 185 average time/residue: 0.9524 time to fit residues: 183.5235 Evaluate side-chains 184 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.215589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.136422 restraints weight = 3690.883| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.36 r_work: 0.3891 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 4700 Z= 0.504 Angle : 0.678 6.380 6260 Z= 0.339 Chirality : 0.046 0.118 660 Planarity : 0.004 0.040 800 Dihedral : 4.725 15.934 700 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 10.25 % Allowed : 31.00 % Favored : 58.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.64 (0.22), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS N 111 PHE 0.008 0.002 PHE R 141 TYR 0.014 0.003 TYR P 128 ARG 0.004 0.001 ARG Q 136 *********************** 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 235 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8519 (mt) REVERT: C 138 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6233 (tp) REVERT: C 140 HIS cc_start: 0.7632 (m-70) cc_final: 0.7208 (m-70) REVERT: Q 136 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8261 (ttm170) REVERT: D 140 HIS cc_start: 0.7447 (m90) cc_final: 0.6836 (m-70) REVERT: H 111 HIS cc_start: 0.7868 (t70) cc_final: 0.7130 (t-90) REVERT: M 140 HIS cc_start: 0.7337 (m90) cc_final: 0.6675 (m-70) REVERT: R 111 HIS cc_start: 0.7864 (t-90) cc_final: 0.7244 (t-90) REVERT: E 129 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8555 (ttt) REVERT: E 134 MET cc_start: 0.7271 (ttm) cc_final: 0.7008 (pmm) REVERT: E 140 HIS cc_start: 0.7554 (m90) cc_final: 0.7127 (m-70) REVERT: I 109 MET cc_start: 0.7586 (mtm) cc_final: 0.7373 (ttm) REVERT: I 111 HIS cc_start: 0.7783 (t70) cc_final: 0.7314 (t-90) REVERT: N 134 MET cc_start: 0.7258 (ttm) cc_final: 0.6948 (pmm) REVERT: N 140 HIS cc_start: 0.7578 (m90) cc_final: 0.7191 (m-70) REVERT: S 109 MET cc_start: 0.7643 (mtm) cc_final: 0.7426 (ttm) REVERT: S 111 HIS cc_start: 0.7774 (t70) cc_final: 0.7245 (t-90) REVERT: S 136 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7763 (mtm180) REVERT: F 138 ILE cc_start: 0.7632 (mt) cc_final: 0.7099 (tp) REVERT: F 140 HIS cc_start: 0.7191 (m90) cc_final: 0.6604 (m90) REVERT: O 138 ILE cc_start: 0.7625 (mt) cc_final: 0.7051 (tp) REVERT: O 140 HIS cc_start: 0.7218 (m90) cc_final: 0.6707 (m-70) outliers start: 41 outliers final: 13 residues processed: 200 average time/residue: 0.9075 time to fit residues: 189.3661 Evaluate side-chains 202 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 H residue 129 MET Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 129 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain T residue 125 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.228835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.151087 restraints weight = 3536.196| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.41 r_work: 0.4023 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4700 Z= 0.226 Angle : 0.562 6.128 6260 Z= 0.275 Chirality : 0.045 0.118 660 Planarity : 0.003 0.039 800 Dihedral : 3.866 13.088 700 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 9.50 % Allowed : 32.25 % Favored : 58.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 111 PHE 0.003 0.001 PHE S 141 TYR 0.007 0.001 TYR B 128 ARG 0.006 0.000 ARG I 136 *********************** 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 : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7186 (ttm) cc_final: 0.6909 (pmm) REVERT: A 138 ILE cc_start: 0.7649 (mt) cc_final: 0.7204 (pp) REVERT: A 140 HIS cc_start: 0.7142 (m-70) cc_final: 0.6764 (m-70) REVERT: B 125 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8526 (mt) REVERT: K 134 MET cc_start: 0.7192 (ttm) cc_final: 0.6909 (pmm) REVERT: K 138 ILE cc_start: 0.7427 (mt) cc_final: 0.7079 (pp) REVERT: C 138 ILE cc_start: 0.6517 (OUTLIER) cc_final: 0.6056 (tp) REVERT: C 140 HIS cc_start: 0.7594 (m-70) cc_final: 0.7176 (m-70) REVERT: L 138 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.5996 (tp) REVERT: L 140 HIS cc_start: 0.7382 (m90) cc_final: 0.6880 (m-70) REVERT: D 140 HIS cc_start: 0.7328 (m90) cc_final: 0.6725 (m-70) REVERT: M 140 HIS cc_start: 0.7293 (m90) cc_final: 0.6665 (m-70) REVERT: E 134 MET cc_start: 0.7056 (ttm) cc_final: 0.6751 (pmm) REVERT: E 140 HIS cc_start: 0.7515 (m90) cc_final: 0.7137 (m-70) REVERT: I 109 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7314 (ttm) REVERT: I 136 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7703 (mtm180) REVERT: N 140 HIS cc_start: 0.7532 (m90) cc_final: 0.7198 (m-70) REVERT: S 109 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7359 (ttm) REVERT: S 136 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.7667 (mtm180) REVERT: O 140 HIS cc_start: 0.7234 (m90) cc_final: 0.6648 (m90) REVERT: T 122 VAL cc_start: 0.6949 (p) cc_final: 0.6596 (t) outliers start: 38 outliers final: 7 residues processed: 192 average time/residue: 0.9650 time to fit residues: 192.9931 Evaluate side-chains 199 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 P residue 121 VAL 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 R residue 108 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain S residue 109 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 140 HIS I 111 HIS S 111 HIS F 140 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.215093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.136898 restraints weight = 3709.849| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.37 r_work: 0.3880 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 4700 Z= 0.559 Angle : 0.725 6.974 6260 Z= 0.351 Chirality : 0.045 0.113 660 Planarity : 0.004 0.037 800 Dihedral : 4.744 16.640 700 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 10.25 % Allowed : 32.50 % 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 (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: -4.74 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 111 PHE 0.008 0.002 PHE R 141 TYR 0.014 0.003 TYR P 128 ARG 0.003 0.001 ARG H 136 *********************** 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 237 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7676 (mt) cc_final: 0.7172 (pp) REVERT: A 140 HIS cc_start: 0.7239 (m-70) cc_final: 0.7029 (m90) REVERT: K 140 HIS cc_start: 0.7252 (m-70) cc_final: 0.7050 (m90) REVERT: C 109 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.6590 (tmt) REVERT: C 138 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.6285 (tp) REVERT: L 109 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.6543 (tmt) REVERT: L 138 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6326 (tp) REVERT: L 140 HIS cc_start: 0.7391 (m90) cc_final: 0.6986 (m-70) REVERT: D 140 HIS cc_start: 0.7368 (m90) cc_final: 0.6632 (m-70) REVERT: M 140 HIS cc_start: 0.7340 (m90) cc_final: 0.6675 (m-70) REVERT: E 140 HIS cc_start: 0.7511 (m90) cc_final: 0.7153 (m-70) REVERT: I 109 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7308 (ttm) REVERT: N 140 HIS cc_start: 0.7505 (m90) cc_final: 0.7092 (m-70) REVERT: S 109 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7320 (ttm) outliers start: 41 outliers final: 19 residues processed: 199 average time/residue: 0.9036 time to fit residues: 187.7463 Evaluate side-chains 217 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 109 MET Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain D residue 125 LEU 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 S residue 109 MET Chi-restraints excluded: chain S residue 134 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain O residue 125 LEU Chi-restraints excluded: chain O residue 130 LEU Chi-restraints excluded: chain T residue 129 MET 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 13 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS I 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.230077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.153603 restraints weight = 3573.564| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.42 r_work: 0.4011 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4700 Z= 0.207 Angle : 0.585 6.906 6260 Z= 0.283 Chirality : 0.045 0.117 660 Planarity : 0.003 0.021 800 Dihedral : 3.817 15.342 700 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 8.25 % Allowed : 33.75 % Favored : 58.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.64 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 140 PHE 0.002 0.000 PHE F 141 TYR 0.007 0.001 TYR P 128 ARG 0.004 0.001 ARG T 136 *********************** 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 216 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7724 (mt) cc_final: 0.7326 (pp) REVERT: K 138 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7236 (pp) REVERT: K 140 HIS cc_start: 0.7166 (m-70) cc_final: 0.6958 (m90) REVERT: P 111 HIS cc_start: 0.7744 (t70) cc_final: 0.7532 (t-90) REVERT: C 138 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.6085 (tp) REVERT: G 136 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7811 (ttm-80) REVERT: L 109 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.6643 (tmt) REVERT: L 138 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.5966 (tp) REVERT: L 140 HIS cc_start: 0.7261 (m90) cc_final: 0.6825 (m-70) REVERT: Q 136 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7824 (ttm-80) REVERT: D 140 HIS cc_start: 0.7344 (m90) cc_final: 0.6647 (m-70) REVERT: M 140 HIS cc_start: 0.7370 (m90) cc_final: 0.6663 (m-70) REVERT: E 140 HIS cc_start: 0.7433 (m90) cc_final: 0.7046 (m-70) REVERT: I 109 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7259 (ttm) REVERT: N 129 MET cc_start: 0.9012 (ttt) cc_final: 0.8630 (ttt) REVERT: N 140 HIS cc_start: 0.7457 (m90) cc_final: 0.7133 (m-70) REVERT: S 109 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7251 (ttm) REVERT: J 122 VAL cc_start: 0.7163 (p) cc_final: 0.6877 (t) REVERT: T 122 VAL cc_start: 0.7153 (p) cc_final: 0.6860 (t) outliers start: 33 outliers final: 4 residues processed: 190 average time/residue: 1.0011 time to fit residues: 197.7420 Evaluate side-chains 192 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 109 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 R residue 108 ASN 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 48 optimal weight: 0.0970 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 overall best weight: 1.0192 ------------------------------------------------------------------------------- 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 = 0.4560 r_free = 0.4560 target = 0.224991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.147641 restraints weight = 3590.028| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.41 r_work: 0.3982 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4700 Z= 0.263 Angle : 0.622 7.089 6260 Z= 0.294 Chirality : 0.043 0.118 660 Planarity : 0.003 0.035 800 Dihedral : 3.879 14.908 700 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 9.00 % Allowed : 31.75 % 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 (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: -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 HIS 0.002 0.001 HIS B 140 PHE 0.004 0.001 PHE Q 141 TYR 0.007 0.001 TYR M 128 ARG 0.007 0.001 ARG H 136 *********************** 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 224 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7256 (pp) REVERT: K 138 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7163 (pp) REVERT: K 140 HIS cc_start: 0.7141 (m-70) cc_final: 0.6910 (m90) REVERT: P 111 HIS cc_start: 0.7784 (t70) cc_final: 0.7571 (t-90) REVERT: C 109 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.6597 (tmt) REVERT: C 138 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5952 (tp) REVERT: G 136 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7791 (ttm-80) REVERT: L 109 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.6595 (tmt) REVERT: L 138 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.5946 (tp) REVERT: L 140 HIS cc_start: 0.7286 (m90) cc_final: 0.6854 (m-70) REVERT: Q 111 HIS cc_start: 0.7723 (t70) cc_final: 0.7404 (t-90) REVERT: D 140 HIS cc_start: 0.7314 (m90) cc_final: 0.6614 (m-70) REVERT: H 111 HIS cc_start: 0.7784 (t-90) cc_final: 0.7232 (t-90) REVERT: M 134 MET cc_start: 0.6866 (ttm) cc_final: 0.6479 (mmm) REVERT: M 140 HIS cc_start: 0.7370 (m90) cc_final: 0.6640 (m-70) REVERT: E 129 MET cc_start: 0.8903 (ttt) cc_final: 0.8387 (ttt) REVERT: E 140 HIS cc_start: 0.7395 (m90) cc_final: 0.6996 (m-70) REVERT: I 109 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7290 (ttm) REVERT: N 129 MET cc_start: 0.8972 (ttt) cc_final: 0.8653 (ttt) REVERT: N 140 HIS cc_start: 0.7437 (m90) cc_final: 0.7089 (m-70) REVERT: S 109 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7307 (ttm) REVERT: J 122 VAL cc_start: 0.6930 (p) cc_final: 0.6676 (t) REVERT: T 122 VAL cc_start: 0.7099 (p) cc_final: 0.6833 (t) outliers start: 36 outliers final: 8 residues processed: 193 average time/residue: 0.9654 time to fit residues: 193.9599 Evaluate side-chains 203 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 109 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 134 MET Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain O residue 125 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 0.0870 chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.223791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.146210 restraints weight = 3589.777| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.41 r_work: 0.3975 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4090 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= 0.312 Angle : 0.646 6.981 6260 Z= 0.307 Chirality : 0.044 0.117 660 Planarity : 0.004 0.039 800 Dihedral : 4.029 14.797 700 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 7.50 % Allowed : 32.00 % Favored : 60.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.59 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS T 140 PHE 0.004 0.001 PHE Q 141 TYR 0.011 0.002 TYR T 128 ARG 0.008 0.001 ARG R 136 *********************** 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 218 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.5451 (tmt) REVERT: A 138 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7264 (pp) REVERT: K 138 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7189 (pp) REVERT: K 140 HIS cc_start: 0.7161 (m-70) cc_final: 0.6959 (m90) REVERT: P 111 HIS cc_start: 0.7788 (t70) cc_final: 0.7550 (t-90) REVERT: C 109 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.6590 (tmt) REVERT: C 138 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.6013 (tp) REVERT: G 111 HIS cc_start: 0.7768 (t70) cc_final: 0.7515 (t-90) REVERT: L 109 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.6619 (tmt) REVERT: L 138 ILE cc_start: 0.6375 (OUTLIER) cc_final: 0.5995 (tp) REVERT: L 140 HIS cc_start: 0.7286 (m90) cc_final: 0.6852 (m-70) REVERT: Q 111 HIS cc_start: 0.7729 (t70) cc_final: 0.7518 (t-90) REVERT: D 134 MET cc_start: 0.7000 (ttm) cc_final: 0.6674 (mmm) REVERT: D 140 HIS cc_start: 0.7354 (m90) cc_final: 0.6631 (m-70) REVERT: M 134 MET cc_start: 0.6856 (ttm) cc_final: 0.6598 (mmm) REVERT: M 140 HIS cc_start: 0.7380 (m90) cc_final: 0.6663 (m-70) REVERT: E 109 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.5916 (tmt) REVERT: E 129 MET cc_start: 0.8905 (ttt) cc_final: 0.8507 (ttt) REVERT: E 140 HIS cc_start: 0.7363 (m90) cc_final: 0.6962 (m-70) REVERT: I 109 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7292 (ttm) REVERT: N 109 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.5795 (tmt) REVERT: N 129 MET cc_start: 0.8935 (ttt) cc_final: 0.8678 (ttt) REVERT: N 140 HIS cc_start: 0.7439 (m90) cc_final: 0.7096 (m-70) REVERT: S 109 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7301 (ttm) REVERT: S 136 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7550 (mtm180) REVERT: J 122 VAL cc_start: 0.7115 (p) cc_final: 0.6874 (t) REVERT: O 109 MET cc_start: 0.7534 (tpt) cc_final: 0.7063 (tpt) outliers start: 30 outliers final: 11 residues processed: 189 average time/residue: 0.9598 time to fit residues: 188.9223 Evaluate side-chains 208 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 109 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 134 MET Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 134 MET Chi-restraints excluded: chain E residue 109 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 J residue 134 MET Chi-restraints excluded: chain O residue 125 LEU 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 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.222153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.144851 restraints weight = 3633.048| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.41 r_work: 0.3972 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4700 Z= 0.343 Angle : 0.667 7.316 6260 Z= 0.316 Chirality : 0.044 0.117 660 Planarity : 0.004 0.044 800 Dihedral : 4.123 15.056 700 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.50 % Allowed : 33.25 % Favored : 60.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS P 140 PHE 0.004 0.001 PHE Q 141 TYR 0.011 0.002 TYR M 128 ARG 0.009 0.001 ARG R 136 *********************** 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 218 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.5695 (tmt) REVERT: A 138 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7281 (pp) REVERT: K 109 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.5660 (tmt) REVERT: K 138 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7185 (pp) REVERT: P 111 HIS cc_start: 0.7812 (t70) cc_final: 0.7577 (t-90) REVERT: C 109 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.6519 (tmt) REVERT: C 138 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.6051 (tp) REVERT: G 111 HIS cc_start: 0.7782 (t70) cc_final: 0.7529 (t-90) REVERT: G 136 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7938 (ttm-80) REVERT: L 109 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.6632 (tmt) REVERT: L 138 ILE cc_start: 0.6345 (OUTLIER) cc_final: 0.5952 (tp) REVERT: L 140 HIS cc_start: 0.7346 (m90) cc_final: 0.6898 (m-70) REVERT: D 134 MET cc_start: 0.6922 (ttm) cc_final: 0.6664 (mmm) REVERT: D 140 HIS cc_start: 0.7371 (m90) cc_final: 0.6615 (m-70) REVERT: M 134 MET cc_start: 0.6835 (ttm) cc_final: 0.6605 (mmm) REVERT: M 140 HIS cc_start: 0.7371 (m90) cc_final: 0.6650 (m-70) REVERT: E 109 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.5797 (tmt) REVERT: E 129 MET cc_start: 0.8875 (ttt) cc_final: 0.8496 (ttt) REVERT: E 140 HIS cc_start: 0.7342 (m90) cc_final: 0.6941 (m-70) REVERT: I 109 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7233 (ttm) REVERT: N 109 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.5985 (tmt) REVERT: N 129 MET cc_start: 0.8957 (ttt) cc_final: 0.8689 (ttt) REVERT: N 140 HIS cc_start: 0.7475 (m90) cc_final: 0.7128 (m-70) REVERT: S 109 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7320 (ttm) REVERT: S 136 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7572 (mtm180) REVERT: J 122 VAL cc_start: 0.7418 (p) cc_final: 0.7186 (t) outliers start: 26 outliers final: 8 residues processed: 192 average time/residue: 0.9486 time to fit residues: 189.8062 Evaluate side-chains 212 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain K residue 109 MET Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 109 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 R residue 108 ASN Chi-restraints excluded: chain R residue 134 MET Chi-restraints excluded: chain E residue 109 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 J residue 134 MET Chi-restraints excluded: chain O residue 125 LEU 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 35 optimal weight: 0.0870 chunk 17 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.4610 r_free = 0.4610 target = 0.236126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.162442 restraints weight = 3552.104| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.42 r_work: 0.4078 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3986 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4700 Z= 0.182 Angle : 0.613 7.618 6260 Z= 0.288 Chirality : 0.045 0.119 660 Planarity : 0.004 0.047 800 Dihedral : 3.571 13.814 700 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 5.25 % Allowed : 35.00 % Favored : 59.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.52 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 111 PHE 0.001 0.000 PHE I 141 TYR 0.014 0.001 TYR J 128 ARG 0.011 0.001 ARG H 136 ********************** 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 208 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.5445 (tmt) REVERT: A 138 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7281 (pp) REVERT: B 136 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7843 (mtp-110) REVERT: K 138 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7248 (pp) REVERT: C 109 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.6460 (tmt) REVERT: G 111 HIS cc_start: 0.7746 (t70) cc_final: 0.7098 (t-90) REVERT: G 136 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7683 (mtt180) REVERT: Q 111 HIS cc_start: 0.7580 (t70) cc_final: 0.6922 (t-90) REVERT: Q 136 ARG cc_start: 0.8092 (ttm170) cc_final: 0.7880 (ttm-80) REVERT: D 140 HIS cc_start: 0.7330 (m90) cc_final: 0.6625 (m-70) REVERT: H 111 HIS cc_start: 0.7739 (t70) cc_final: 0.7072 (t-90) REVERT: H 136 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7575 (mtm180) REVERT: M 140 HIS cc_start: 0.7329 (m90) cc_final: 0.6692 (m-70) REVERT: R 111 HIS cc_start: 0.7757 (t-90) cc_final: 0.7055 (t-90) REVERT: R 136 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7498 (mtm180) REVERT: E 129 MET cc_start: 0.8830 (ttt) cc_final: 0.8554 (ttt) REVERT: E 140 HIS cc_start: 0.7385 (m90) cc_final: 0.7011 (m-70) REVERT: I 109 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7324 (ttm) REVERT: N 140 HIS cc_start: 0.7463 (m90) cc_final: 0.7087 (m-70) REVERT: S 109 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7346 (ttm) REVERT: S 136 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7549 (mtm180) REVERT: F 138 ILE cc_start: 0.7672 (mt) cc_final: 0.7314 (pt) REVERT: J 136 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7433 (mtt180) REVERT: O 140 HIS cc_start: 0.7162 (m-70) cc_final: 0.6679 (m90) REVERT: T 136 ARG cc_start: 0.8019 (ttp-110) cc_final: 0.7306 (mtt180) outliers start: 21 outliers final: 5 residues processed: 187 average time/residue: 0.9669 time to fit residues: 188.3322 Evaluate side-chains 195 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain P residue 122 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 S residue 109 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 0.0270 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 140 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 = 0.4540 r_free = 0.4540 target = 0.221453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.144507 restraints weight = 3641.718| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.38 r_work: 0.3961 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4700 Z= 0.343 Angle : 0.684 7.716 6260 Z= 0.322 Chirality : 0.044 0.120 660 Planarity : 0.004 0.047 800 Dihedral : 4.048 14.709 700 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % 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 (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: -4.57 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 140 PHE 0.005 0.001 PHE P 141 TYR 0.013 0.002 TYR M 128 ARG 0.010 0.001 ARG P 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4984.88 seconds wall clock time: 85 minutes 17.83 seconds (5117.83 seconds total)