Starting phenix.real_space_refine on Sun Mar 10 19:56:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/03_2024/7rl4_24514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/03_2024/7rl4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/03_2024/7rl4_24514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/03_2024/7rl4_24514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/03_2024/7rl4_24514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/03_2024/7rl4_24514.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.85, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 1.78 Conformation dependent library (CDL) restraints added in 905.7 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: 0.59 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: 1.02 Time building geometry restraints manager: 1.92 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: 98.68 - 105.22: 140 105.22 - 111.76: 2171 111.76 - 118.30: 1389 118.30 - 124.84: 2500 124.84 - 131.38: 60 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 2.440 nonbonded pdb=" OG SER B 132 " pdb=" O LEU S 130 " model vdw 2.535 2.440 nonbonded pdb=" O LEU P 130 " pdb=" OG SER H 132 " model vdw 2.535 2.440 nonbonded pdb=" OG SER G 132 " pdb=" O LEU R 130 " model vdw 2.535 2.440 nonbonded pdb=" OG SER S 132 " pdb=" O LEU J 130 " model vdw 2.536 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.550 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.960 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.870 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.471 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: 1.0561 time to fit residues: 200.5175 Evaluate side-chains 162 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4700 Z= 0.205 Angle : 0.567 6.184 6260 Z= 0.284 Chirality : 0.045 0.119 660 Planarity : 0.003 0.021 800 Dihedral : 4.137 14.982 702 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 9.75 % Allowed : 20.50 % Favored : 69.75 % 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: -4.58 (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 0.003 0.001 HIS K 111 PHE 0.004 0.001 PHE K 141 TYR 0.010 0.001 TYR O 128 ARG 0.004 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 fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 HIS cc_start: 0.7449 (m90) cc_final: 0.7075 (m-70) REVERT: K 140 HIS cc_start: 0.7373 (m90) cc_final: 0.7000 (m-70) REVERT: L 138 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6439 (pp) REVERT: L 140 HIS cc_start: 0.7616 (m90) cc_final: 0.7271 (m-70) REVERT: D 140 HIS cc_start: 0.7597 (m90) cc_final: 0.7002 (m-70) REVERT: H 111 HIS cc_start: 0.7687 (t70) cc_final: 0.6996 (t-90) REVERT: M 140 HIS cc_start: 0.7509 (m90) cc_final: 0.6943 (m-70) REVERT: R 111 HIS cc_start: 0.7670 (t70) cc_final: 0.6940 (t-90) REVERT: E 140 HIS cc_start: 0.7709 (m90) cc_final: 0.7343 (m-70) REVERT: I 111 HIS cc_start: 0.7711 (t70) cc_final: 0.7116 (t-90) REVERT: I 136 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7270 (mtm180) REVERT: N 140 HIS cc_start: 0.7627 (m90) cc_final: 0.7258 (m-70) REVERT: S 111 HIS cc_start: 0.7691 (t70) cc_final: 0.7086 (t-90) REVERT: S 136 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7270 (mtm180) REVERT: F 138 ILE cc_start: 0.7943 (mt) cc_final: 0.7403 (tp) REVERT: F 140 HIS cc_start: 0.7397 (m90) cc_final: 0.6933 (m-70) REVERT: J 136 ARG cc_start: 0.7621 (ttp-110) cc_final: 0.7184 (mtm180) REVERT: O 138 ILE cc_start: 0.7874 (mt) cc_final: 0.7240 (tp) REVERT: O 140 HIS cc_start: 0.7364 (m90) cc_final: 0.6910 (m-70) REVERT: T 136 ARG cc_start: 0.7643 (ttp-110) cc_final: 0.7162 (mtm180) outliers start: 39 outliers final: 10 residues processed: 185 average time/residue: 0.9695 time to fit residues: 186.7138 Evaluate side-chains 188 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain S residue 134 MET Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain T residue 129 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 0.0980 chunk 45 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS R 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 4700 Z= 0.452 Angle : 0.656 6.623 6260 Z= 0.327 Chirality : 0.045 0.116 660 Planarity : 0.004 0.042 800 Dihedral : 4.580 14.639 700 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 9.75 % Allowed : 30.75 % Favored : 59.50 % 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: -4.58 (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 0.004 0.002 HIS E 111 PHE 0.009 0.002 PHE R 141 TYR 0.012 0.003 TYR P 128 ARG 0.004 0.001 ARG G 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 223 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 HIS cc_start: 0.7362 (m90) cc_final: 0.6984 (m-70) REVERT: K 140 HIS cc_start: 0.7333 (m90) cc_final: 0.6961 (m-70) REVERT: C 138 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6326 (tp) REVERT: C 140 HIS cc_start: 0.7708 (m-70) cc_final: 0.7310 (m-70) REVERT: L 138 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6473 (pp) REVERT: L 140 HIS cc_start: 0.7582 (m90) cc_final: 0.7251 (m-70) REVERT: D 140 HIS cc_start: 0.7574 (m90) cc_final: 0.6979 (m-70) REVERT: H 111 HIS cc_start: 0.7822 (t-90) cc_final: 0.7236 (t-90) REVERT: M 140 HIS cc_start: 0.7415 (m90) cc_final: 0.6801 (m-70) REVERT: R 111 HIS cc_start: 0.7798 (t-90) cc_final: 0.7219 (t-90) REVERT: E 140 HIS cc_start: 0.7665 (m90) cc_final: 0.7231 (m-70) REVERT: I 111 HIS cc_start: 0.7759 (t70) cc_final: 0.7312 (t-90) REVERT: I 136 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7360 (mtm180) REVERT: N 140 HIS cc_start: 0.7658 (m90) cc_final: 0.7232 (m-70) REVERT: S 136 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7382 (mtm180) REVERT: F 138 ILE cc_start: 0.7872 (mt) cc_final: 0.7334 (tp) REVERT: F 140 HIS cc_start: 0.7349 (m90) cc_final: 0.6910 (m-70) REVERT: O 138 ILE cc_start: 0.7825 (mt) cc_final: 0.7261 (tp) REVERT: O 140 HIS cc_start: 0.7327 (m90) cc_final: 0.6861 (m-70) outliers start: 39 outliers final: 13 residues processed: 192 average time/residue: 0.9149 time to fit residues: 183.3147 Evaluate side-chains 193 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 178 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 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 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 N 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 41 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS P 111 HIS E 140 HIS N 140 HIS S 111 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.156 4700 Z= 0.855 Angle : 0.860 7.525 6260 Z= 0.432 Chirality : 0.051 0.182 660 Planarity : 0.006 0.042 800 Dihedral : 5.505 17.933 700 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 12.75 % Allowed : 26.75 % 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: -4.77 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 111 PHE 0.012 0.002 PHE R 141 TYR 0.018 0.004 TYR P 128 ARG 0.004 0.002 ARG D 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 252 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 201 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8483 (mt) REVERT: K 134 MET cc_start: 0.6159 (pmm) cc_final: 0.5953 (pmm) REVERT: P 125 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8439 (mt) REVERT: C 138 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6480 (pp) REVERT: L 138 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.6352 (pp) REVERT: L 140 HIS cc_start: 0.7655 (m90) cc_final: 0.7229 (m-70) REVERT: Q 111 HIS cc_start: 0.7559 (t70) cc_final: 0.7352 (t-90) REVERT: D 138 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7528 (pp) REVERT: D 140 HIS cc_start: 0.7402 (m90) cc_final: 0.6753 (m-70) REVERT: M 138 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7594 (pp) REVERT: M 140 HIS cc_start: 0.7335 (m90) cc_final: 0.6719 (m-70) REVERT: E 140 HIS cc_start: 0.7501 (m-70) cc_final: 0.7153 (m-70) REVERT: I 111 HIS cc_start: 0.7798 (t70) cc_final: 0.7309 (t-90) REVERT: N 140 HIS cc_start: 0.7453 (m-70) cc_final: 0.7028 (m-70) REVERT: F 138 ILE cc_start: 0.7814 (mt) cc_final: 0.7342 (tp) REVERT: O 138 ILE cc_start: 0.7712 (mt) cc_final: 0.7174 (tp) REVERT: O 140 HIS cc_start: 0.7246 (m90) cc_final: 0.6719 (m90) outliers start: 51 outliers final: 16 residues processed: 216 average time/residue: 0.9371 time to fit residues: 210.9738 Evaluate side-chains 213 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 L residue 125 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain Q residue 134 MET Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 128 TYR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain O residue 130 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4700 Z= 0.244 Angle : 0.600 6.937 6260 Z= 0.293 Chirality : 0.045 0.116 660 Planarity : 0.003 0.024 800 Dihedral : 4.006 15.780 700 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 9.75 % Allowed : 31.25 % 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 (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: -4.60 (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 0.002 0.000 HIS P 140 PHE 0.003 0.001 PHE S 141 TYR 0.006 0.001 TYR D 128 ARG 0.003 0.000 ARG B 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 229 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7750 (mt) cc_final: 0.7472 (pp) REVERT: B 111 HIS cc_start: 0.7765 (t70) cc_final: 0.7493 (t-90) REVERT: K 138 ILE cc_start: 0.7663 (mt) cc_final: 0.7376 (pp) REVERT: P 111 HIS cc_start: 0.7746 (t70) cc_final: 0.7454 (t-90) REVERT: C 138 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.6047 (tp) REVERT: C 140 HIS cc_start: 0.7635 (m-70) cc_final: 0.7104 (m-70) REVERT: L 138 ILE cc_start: 0.6512 (OUTLIER) cc_final: 0.6097 (pp) REVERT: L 140 HIS cc_start: 0.7414 (m-70) cc_final: 0.7188 (m-70) REVERT: Q 111 HIS cc_start: 0.7633 (t70) cc_final: 0.7383 (t-90) REVERT: D 140 HIS cc_start: 0.7436 (m90) cc_final: 0.6812 (m-70) REVERT: M 140 HIS cc_start: 0.7379 (m90) cc_final: 0.6771 (m-70) REVERT: E 140 HIS cc_start: 0.7580 (m-70) cc_final: 0.7163 (m-70) REVERT: N 140 HIS cc_start: 0.7492 (m-70) cc_final: 0.7095 (m-70) REVERT: T 109 MET cc_start: 0.6588 (mtp) cc_final: 0.6089 (mtp) outliers start: 39 outliers final: 8 residues processed: 197 average time/residue: 0.9876 time to fit residues: 202.7486 Evaluate side-chains 195 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain P residue 112 MET Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 125 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS K 140 HIS I 111 HIS S 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 4700 Z= 0.522 Angle : 0.704 7.015 6260 Z= 0.347 Chirality : 0.044 0.114 660 Planarity : 0.004 0.028 800 Dihedral : 4.661 15.636 700 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: -4.68 (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 HIS 0.003 0.001 HIS D 111 PHE 0.007 0.001 PHE H 141 TYR 0.012 0.003 TYR M 128 ARG 0.003 0.001 ARG P 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 235 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 197 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 HIS cc_start: 0.7072 (m170) cc_final: 0.6846 (m-70) REVERT: B 111 HIS cc_start: 0.7801 (t70) cc_final: 0.7496 (t-90) REVERT: K 140 HIS cc_start: 0.7033 (m170) cc_final: 0.6816 (m-70) REVERT: P 111 HIS cc_start: 0.7863 (t70) cc_final: 0.7585 (t-90) REVERT: C 138 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.6125 (tp) REVERT: C 140 HIS cc_start: 0.7592 (m-70) cc_final: 0.7115 (m-70) REVERT: L 140 HIS cc_start: 0.7517 (m-70) cc_final: 0.7255 (m-70) REVERT: D 140 HIS cc_start: 0.7444 (m90) cc_final: 0.6864 (m-70) REVERT: M 138 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7028 (tp) REVERT: M 140 HIS cc_start: 0.7406 (m90) cc_final: 0.6780 (m-70) REVERT: E 140 HIS cc_start: 0.7567 (m-70) cc_final: 0.7165 (m-70) REVERT: N 140 HIS cc_start: 0.7480 (m-70) cc_final: 0.7084 (m-70) outliers start: 38 outliers final: 17 residues processed: 212 average time/residue: 0.9220 time to fit residues: 203.7016 Evaluate side-chains 215 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 L residue 125 LEU Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain S residue 132 SER Chi-restraints excluded: chain S residue 136 ARG Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain O residue 130 LEU Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 140 HIS I 111 HIS N 140 HIS S 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 4700 Z= 0.518 Angle : 0.738 7.722 6260 Z= 0.359 Chirality : 0.044 0.115 660 Planarity : 0.004 0.028 800 Dihedral : 4.761 17.310 700 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 8.75 % Allowed : 31.75 % Favored : 59.50 % 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: -4.73 (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 0.003 0.001 HIS T 140 PHE 0.006 0.001 PHE Q 141 TYR 0.013 0.002 TYR M 128 ARG 0.003 0.001 ARG C 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 228 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7411 (pp) REVERT: A 140 HIS cc_start: 0.7054 (m170) cc_final: 0.6801 (m-70) REVERT: B 111 HIS cc_start: 0.7849 (t70) cc_final: 0.7596 (t-90) REVERT: K 140 HIS cc_start: 0.7001 (m170) cc_final: 0.6717 (m-70) REVERT: P 111 HIS cc_start: 0.7843 (t70) cc_final: 0.7544 (t-90) REVERT: C 138 ILE cc_start: 0.6452 (OUTLIER) cc_final: 0.6151 (tp) REVERT: C 140 HIS cc_start: 0.7536 (m-70) cc_final: 0.7083 (m-70) REVERT: L 109 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.6379 (tmt) REVERT: L 138 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6225 (tp) REVERT: L 140 HIS cc_start: 0.7552 (m-70) cc_final: 0.7199 (m-70) REVERT: D 140 HIS cc_start: 0.7502 (m90) cc_final: 0.6846 (m-70) REVERT: M 140 HIS cc_start: 0.7461 (m90) cc_final: 0.6838 (m-70) REVERT: E 140 HIS cc_start: 0.7460 (m90) cc_final: 0.7174 (m-70) REVERT: N 129 MET cc_start: 0.9006 (ttt) cc_final: 0.8344 (ttt) REVERT: N 140 HIS cc_start: 0.7422 (m90) cc_final: 0.7124 (m-70) outliers start: 35 outliers final: 21 residues processed: 199 average time/residue: 0.9432 time to fit residues: 195.5238 Evaluate side-chains 215 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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 125 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain S residue 132 SER Chi-restraints excluded: chain S residue 136 ARG Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain O residue 130 LEU Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 0.0570 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 0.2980 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4262 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= 0.187 Angle : 0.594 7.117 6260 Z= 0.285 Chirality : 0.045 0.118 660 Planarity : 0.003 0.024 800 Dihedral : 3.753 15.518 700 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 7.25 % Allowed : 33.75 % 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 (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 0.000 HIS N 111 PHE 0.002 0.000 PHE O 141 TYR 0.011 0.001 TYR J 128 ARG 0.003 0.000 ARG J 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 213 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7474 (pp) REVERT: A 140 HIS cc_start: 0.7031 (m170) cc_final: 0.6769 (m-70) REVERT: B 111 HIS cc_start: 0.7760 (t70) cc_final: 0.7465 (t-90) REVERT: K 138 ILE cc_start: 0.7737 (mt) cc_final: 0.7404 (pp) REVERT: K 140 HIS cc_start: 0.6992 (m170) cc_final: 0.6762 (m-70) REVERT: P 111 HIS cc_start: 0.7738 (t70) cc_final: 0.7459 (t-90) REVERT: C 138 ILE cc_start: 0.6366 (OUTLIER) cc_final: 0.5956 (tp) REVERT: C 140 HIS cc_start: 0.7449 (m-70) cc_final: 0.7003 (m-70) REVERT: L 138 ILE cc_start: 0.6388 (OUTLIER) cc_final: 0.6161 (tp) REVERT: D 140 HIS cc_start: 0.7495 (m90) cc_final: 0.6917 (m-70) REVERT: M 140 HIS cc_start: 0.7448 (m90) cc_final: 0.7093 (m-70) REVERT: E 140 HIS cc_start: 0.7529 (m90) cc_final: 0.7221 (m-70) REVERT: N 129 MET cc_start: 0.9041 (ttt) cc_final: 0.8499 (ttt) REVERT: N 140 HIS cc_start: 0.7530 (m90) cc_final: 0.7216 (m-70) outliers start: 29 outliers final: 3 residues processed: 191 average time/residue: 1.0096 time to fit residues: 200.4968 Evaluate side-chains 190 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain I residue 134 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 4700 Z= 0.515 Angle : 0.753 7.591 6260 Z= 0.362 Chirality : 0.045 0.117 660 Planarity : 0.004 0.034 800 Dihedral : 4.647 16.995 700 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 6.00 % Allowed : 33.25 % Favored : 60.75 % 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: -4.65 (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 HIS 0.003 0.001 HIS T 140 PHE 0.006 0.001 PHE H 141 TYR 0.012 0.002 TYR P 128 ARG 0.003 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 219 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6152 (tmt) REVERT: A 138 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7432 (pp) REVERT: B 111 HIS cc_start: 0.7809 (t70) cc_final: 0.7496 (t-90) REVERT: K 138 ILE cc_start: 0.7699 (mt) cc_final: 0.7343 (pp) REVERT: K 140 HIS cc_start: 0.7007 (m170) cc_final: 0.6743 (m-70) REVERT: P 111 HIS cc_start: 0.7838 (t70) cc_final: 0.7538 (t-90) REVERT: C 109 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6217 (tmt) REVERT: C 138 ILE cc_start: 0.6400 (OUTLIER) cc_final: 0.6097 (pp) REVERT: C 140 HIS cc_start: 0.7537 (m-70) cc_final: 0.7069 (m-70) REVERT: L 109 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6429 (tmt) REVERT: Q 109 MET cc_start: 0.6593 (mtp) cc_final: 0.6358 (mtm) REVERT: D 140 HIS cc_start: 0.7524 (m90) cc_final: 0.6902 (m-70) REVERT: M 140 HIS cc_start: 0.7472 (m90) cc_final: 0.6859 (m-70) REVERT: E 109 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.5963 (tmt) REVERT: E 140 HIS cc_start: 0.7507 (m90) cc_final: 0.7166 (m-70) REVERT: N 109 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.5919 (tmt) REVERT: N 140 HIS cc_start: 0.7531 (m90) cc_final: 0.7181 (m-70) REVERT: F 109 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7341 (tpt) REVERT: O 109 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7355 (tpt) outliers start: 24 outliers final: 10 residues processed: 198 average time/residue: 0.9173 time to fit residues: 189.4768 Evaluate side-chains 211 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain P residue 121 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 D residue 134 MET 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 E 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 134 MET Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain O 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 4 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS G 108 ASN I 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4700 Z= 0.240 Angle : 0.671 7.377 6260 Z= 0.315 Chirality : 0.045 0.121 660 Planarity : 0.003 0.022 800 Dihedral : 3.955 14.627 700 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 5.75 % Allowed : 32.00 % Favored : 62.25 % 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: -4.55 (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 HIS 0.002 0.000 HIS E 111 PHE 0.002 0.001 PHE C 141 TYR 0.012 0.001 TYR J 128 ARG 0.003 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 205 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.5691 (tmt) REVERT: B 111 HIS cc_start: 0.7774 (t70) cc_final: 0.7471 (t-90) REVERT: K 138 ILE cc_start: 0.7740 (mt) cc_final: 0.7393 (pp) REVERT: K 140 HIS cc_start: 0.6998 (m170) cc_final: 0.6698 (m-70) REVERT: P 111 HIS cc_start: 0.7705 (t70) cc_final: 0.7407 (t-90) REVERT: L 109 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6460 (tmt) REVERT: Q 109 MET cc_start: 0.6533 (mtp) cc_final: 0.6170 (mmm) REVERT: D 140 HIS cc_start: 0.7507 (m90) cc_final: 0.6878 (m-70) REVERT: M 140 HIS cc_start: 0.7491 (m90) cc_final: 0.6871 (m-70) REVERT: E 109 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6044 (tmt) REVERT: E 140 HIS cc_start: 0.7557 (m90) cc_final: 0.7237 (m-70) REVERT: N 109 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.5936 (tmt) REVERT: N 129 MET cc_start: 0.9059 (ttt) cc_final: 0.8515 (ttt) REVERT: N 140 HIS cc_start: 0.7555 (m90) cc_final: 0.7225 (m-70) REVERT: F 109 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7211 (tpt) REVERT: O 109 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7205 (tpt) outliers start: 23 outliers final: 6 residues processed: 184 average time/residue: 0.9986 time to fit residues: 191.1326 Evaluate side-chains 194 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain L residue 109 MET Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain O 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 48 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 HIS R 111 HIS I 111 HIS S 111 HIS F 140 HIS J 111 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.204597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.129412 restraints weight = 3777.362| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.32 r_work: 0.3814 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.157 4700 Z= 1.105 Angle : 1.064 8.282 6260 Z= 0.525 Chirality : 0.058 0.205 660 Planarity : 0.007 0.065 800 Dihedral : 5.874 18.623 700 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 7.25 % Allowed : 33.50 % 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: -4.77 (0.22), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.17), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 111 PHE 0.016 0.003 PHE P 141 TYR 0.024 0.005 TYR P 128 ARG 0.005 0.001 ARG Q 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3189.15 seconds wall clock time: 56 minutes 33.58 seconds (3393.58 seconds total)