Starting phenix.real_space_refine on Tue Feb 11 07:09:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rl4_24514/02_2025/7rl4_24514.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rl4_24514/02_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_24514/02_2025/7rl4_24514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rl4_24514/02_2025/7rl4_24514.map" model { file = "/net/cci-nas-00/data/ceres_data/7rl4_24514/02_2025/7rl4_24514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rl4_24514/02_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-5592/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: 3.47, per 1000 atoms: 0.75 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: 1.12 Conformation dependent library (CDL) restraints added in 572.1 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: 0.69 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: 1.27 Time building geometry restraints manager: 1.31 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: 0.780 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.450 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.380 ------------------------------------------------------------------------------- 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 : 0.486 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: 1.1461 time to fit residues: 217.4968 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 : 0.497 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 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: 0.3956 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7340 (ttm) cc_final: 0.6915 (pmm) REVERT: A 140 HIS cc_start: 0.7312 (m90) cc_final: 0.6950 (m-70) REVERT: K 134 MET cc_start: 0.7334 (ttm) cc_final: 0.6917 (pmm) REVERT: K 140 HIS cc_start: 0.7305 (m90) cc_final: 0.6944 (m-70) REVERT: L 138 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6513 (pp) REVERT: D 140 HIS cc_start: 0.7487 (m90) cc_final: 0.6912 (m-70) REVERT: H 111 HIS cc_start: 0.7781 (t70) cc_final: 0.7081 (t-90) REVERT: M 140 HIS cc_start: 0.7365 (m90) cc_final: 0.6785 (m-70) REVERT: R 111 HIS cc_start: 0.7772 (t70) cc_final: 0.6969 (t-90) REVERT: E 134 MET cc_start: 0.7337 (ttm) cc_final: 0.6879 (pmm) REVERT: E 140 HIS cc_start: 0.7600 (m90) cc_final: 0.7235 (m-70) REVERT: I 111 HIS cc_start: 0.7713 (t70) cc_final: 0.7113 (t-90) REVERT: I 136 ARG cc_start: 0.8246 (ttm-80) cc_final: 0.7617 (mtm180) REVERT: N 134 MET cc_start: 0.7357 (ttm) cc_final: 0.6933 (pmm) REVERT: N 140 HIS cc_start: 0.7540 (m90) cc_final: 0.7178 (m-70) REVERT: S 111 HIS cc_start: 0.7715 (t70) cc_final: 0.7070 (t-90) REVERT: S 136 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7592 (mtm180) REVERT: F 138 ILE cc_start: 0.7687 (mt) cc_final: 0.7110 (tp) REVERT: F 140 HIS cc_start: 0.7211 (m90) cc_final: 0.6674 (m-70) REVERT: J 111 HIS cc_start: 0.7667 (t70) cc_final: 0.7028 (t70) REVERT: J 136 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7578 (mtm180) REVERT: O 138 ILE cc_start: 0.7641 (mt) cc_final: 0.6987 (tp) REVERT: O 140 HIS cc_start: 0.7249 (m90) cc_final: 0.6738 (m-70) outliers start: 39 outliers final: 7 residues processed: 185 average time/residue: 0.9706 time to fit residues: 186.9804 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 : 0.472 ------------------------------------------------------------------------------- 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: 6.9990 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.215452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.135497 restraints weight = 3664.421| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.39 r_work: 0.3894 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 4700 Z= 0.509 Angle : 0.684 6.516 6260 Z= 0.341 Chirality : 0.046 0.118 660 Planarity : 0.004 0.042 800 Dihedral : 4.733 15.698 700 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 10.50 % Allowed : 30.75 % 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: -4.63 (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 K 111 PHE 0.009 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 236 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8545 (mt) REVERT: C 138 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6255 (tp) REVERT: C 140 HIS cc_start: 0.7638 (m-70) cc_final: 0.7239 (m-70) REVERT: Q 136 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.8258 (ttm170) REVERT: D 140 HIS cc_start: 0.7464 (m90) cc_final: 0.6852 (m-70) REVERT: H 111 HIS cc_start: 0.7882 (t70) cc_final: 0.7150 (t-90) REVERT: M 140 HIS cc_start: 0.7351 (m90) cc_final: 0.6689 (m-70) REVERT: R 111 HIS cc_start: 0.7861 (t70) cc_final: 0.7106 (t-90) REVERT: E 129 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8562 (ttt) REVERT: E 134 MET cc_start: 0.7245 (ttm) cc_final: 0.7034 (pmm) REVERT: E 140 HIS cc_start: 0.7576 (m90) cc_final: 0.7118 (m-70) REVERT: I 109 MET cc_start: 0.7584 (mtm) cc_final: 0.7374 (ttm) REVERT: I 111 HIS cc_start: 0.7804 (t70) cc_final: 0.7338 (t-90) REVERT: I 136 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.7741 (mtm180) REVERT: N 134 MET cc_start: 0.7249 (ttm) cc_final: 0.6962 (pmm) REVERT: N 140 HIS cc_start: 0.7600 (m90) cc_final: 0.7210 (m-70) REVERT: S 109 MET cc_start: 0.7651 (mtm) cc_final: 0.7436 (ttm) REVERT: S 111 HIS cc_start: 0.7791 (t70) cc_final: 0.7269 (t-90) REVERT: S 136 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7770 (mtm180) REVERT: F 138 ILE cc_start: 0.7652 (mt) cc_final: 0.7120 (tp) REVERT: F 140 HIS cc_start: 0.7223 (m90) cc_final: 0.6643 (m90) REVERT: O 138 ILE cc_start: 0.7647 (mt) cc_final: 0.7074 (tp) REVERT: O 140 HIS cc_start: 0.7247 (m90) cc_final: 0.6736 (m-70) outliers start: 42 outliers final: 13 residues processed: 200 average time/residue: 0.9630 time to fit residues: 200.6976 Evaluate side-chains 204 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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: 0.9990 chunk 43 optimal weight: 0.0970 chunk 44 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 chunk 19 optimal weight: 0.0570 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 R 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.234485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.157816 restraints weight = 3511.760| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.42 r_work: 0.4043 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4700 Z= 0.173 Angle : 0.539 6.276 6260 Z= 0.262 Chirality : 0.045 0.119 660 Planarity : 0.002 0.022 800 Dihedral : 3.700 13.688 700 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 9.00 % Allowed : 31.25 % 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: -4.60 (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 111 PHE 0.002 0.000 PHE S 141 TYR 0.006 0.001 TYR C 128 ARG 0.004 0.000 ARG Q 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 225 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7204 (ttm) cc_final: 0.6926 (pmm) REVERT: A 138 ILE cc_start: 0.7710 (mt) cc_final: 0.7275 (pp) REVERT: A 140 HIS cc_start: 0.7174 (m-70) cc_final: 0.6845 (m-70) REVERT: K 134 MET cc_start: 0.7183 (ttm) cc_final: 0.6894 (pmm) REVERT: K 138 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7156 (pp) REVERT: K 140 HIS cc_start: 0.7178 (m-70) cc_final: 0.6913 (m-70) REVERT: C 138 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.6023 (tp) REVERT: C 140 HIS cc_start: 0.7623 (m-70) cc_final: 0.7237 (m-70) REVERT: L 138 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.6128 (tp) REVERT: D 140 HIS cc_start: 0.7353 (m90) cc_final: 0.6752 (m-70) REVERT: M 140 HIS cc_start: 0.7348 (m90) cc_final: 0.6710 (m-70) REVERT: E 140 HIS cc_start: 0.7492 (m90) cc_final: 0.7095 (m-70) REVERT: I 109 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7271 (ttm) REVERT: I 136 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7676 (mtm180) REVERT: N 140 HIS cc_start: 0.7501 (m90) cc_final: 0.7077 (m-70) REVERT: S 109 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7290 (ttm) REVERT: S 111 HIS cc_start: 0.7779 (t70) cc_final: 0.7284 (t-90) REVERT: S 136 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7658 (mtm180) REVERT: F 112 MET cc_start: 0.8726 (ttt) cc_final: 0.8447 (ttt) REVERT: J 136 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7499 (mtm180) REVERT: O 140 HIS cc_start: 0.7259 (m90) cc_final: 0.6758 (m-70) REVERT: T 122 VAL cc_start: 0.6669 (p) cc_final: 0.6335 (t) REVERT: T 134 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7337 (ttm) REVERT: T 136 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7411 (mtt180) outliers start: 36 outliers final: 6 residues processed: 193 average time/residue: 1.0029 time to fit residues: 201.2972 Evaluate side-chains 198 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU 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 121 VAL Chi-restraints excluded: chain C residue 138 ILE 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 I residue 109 MET Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain T residue 134 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 F 140 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.211215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.133025 restraints weight = 3744.361| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.36 r_work: 0.3843 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.112 4700 Z= 0.710 Angle : 0.789 6.832 6260 Z= 0.385 Chirality : 0.047 0.118 660 Planarity : 0.005 0.031 800 Dihedral : 4.997 16.666 700 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 9.75 % Allowed : 33.50 % Favored : 56.75 % 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: -4.80 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 111 PHE 0.011 0.002 PHE H 141 TYR 0.018 0.004 TYR B 128 ARG 0.003 0.001 ARG R 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 231 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7653 (mt) cc_final: 0.7147 (pp) REVERT: A 140 HIS cc_start: 0.7226 (m-70) cc_final: 0.7021 (m90) REVERT: C 138 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6188 (pp) REVERT: L 138 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6379 (tp) REVERT: L 140 HIS cc_start: 0.7411 (m90) cc_final: 0.7024 (m-70) REVERT: Q 111 HIS cc_start: 0.7724 (t70) cc_final: 0.7368 (t-90) REVERT: D 109 MET cc_start: 0.7296 (tpt) cc_final: 0.5922 (tpt) REVERT: D 140 HIS cc_start: 0.7349 (m90) cc_final: 0.6658 (m-70) REVERT: M 140 HIS cc_start: 0.7295 (m90) cc_final: 0.6616 (m-70) REVERT: E 140 HIS cc_start: 0.7502 (m90) cc_final: 0.7126 (m-70) REVERT: I 109 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7333 (ttm) REVERT: N 129 MET cc_start: 0.8637 (ttm) cc_final: 0.8199 (ttt) REVERT: N 140 HIS cc_start: 0.7531 (m90) cc_final: 0.7099 (m-70) REVERT: S 109 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7374 (ttm) REVERT: S 111 HIS cc_start: 0.7829 (t70) cc_final: 0.7275 (t-90) REVERT: F 138 ILE cc_start: 0.7631 (mt) cc_final: 0.7102 (tp) REVERT: J 109 MET cc_start: 0.7733 (mtt) cc_final: 0.7421 (mtp) REVERT: O 138 ILE cc_start: 0.7628 (mt) cc_final: 0.7107 (tp) outliers start: 39 outliers final: 19 residues processed: 197 average time/residue: 0.9631 time to fit residues: 197.6784 Evaluate side-chains 210 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 D residue 125 LEU Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 129 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain N residue 125 LEU 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 134 MET Chi-restraints excluded: chain O residue 125 LEU Chi-restraints excluded: chain O residue 130 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4585 r_free = 0.4585 target = 0.231291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.155808 restraints weight = 3557.498| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.41 r_work: 0.4029 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4700 Z= 0.199 Angle : 0.596 6.791 6260 Z= 0.284 Chirality : 0.045 0.119 660 Planarity : 0.003 0.023 800 Dihedral : 3.825 15.283 700 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 8.00 % Allowed : 34.75 % 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: -4.68 (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 0.001 0.000 HIS K 140 PHE 0.002 0.000 PHE P 141 TYR 0.007 0.001 TYR M 128 ARG 0.004 0.001 ARG R 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 215 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7272 (pp) REVERT: K 134 MET cc_start: 0.6231 (pmm) cc_final: 0.5786 (pmm) REVERT: K 138 ILE cc_start: 0.7490 (mt) cc_final: 0.7232 (pp) REVERT: C 138 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.6065 (tp) REVERT: L 138 ILE cc_start: 0.6371 (OUTLIER) cc_final: 0.5986 (tp) REVERT: L 140 HIS cc_start: 0.7274 (m90) cc_final: 0.6846 (m-70) REVERT: D 140 HIS cc_start: 0.7371 (m90) cc_final: 0.6646 (m-70) REVERT: M 134 MET cc_start: 0.6831 (ttm) cc_final: 0.6357 (mmm) REVERT: M 140 HIS cc_start: 0.7324 (m90) cc_final: 0.6706 (m-70) REVERT: E 140 HIS cc_start: 0.7443 (m90) cc_final: 0.7056 (m-70) REVERT: I 109 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7259 (ttm) REVERT: N 140 HIS cc_start: 0.7432 (m90) cc_final: 0.7077 (m-70) REVERT: S 109 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7360 (ttm) REVERT: J 122 VAL cc_start: 0.6748 (p) cc_final: 0.6506 (t) REVERT: T 122 VAL cc_start: 0.6995 (p) cc_final: 0.6754 (t) outliers start: 32 outliers final: 5 residues processed: 189 average time/residue: 1.0451 time to fit residues: 205.1861 Evaluate side-chains 190 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain H residue 108 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.3980 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 140 HIS I 108 ASN I 111 HIS S 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.213088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.136021 restraints weight = 3686.641| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.35 r_work: 0.3874 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 4700 Z= 0.615 Angle : 0.774 7.317 6260 Z= 0.371 Chirality : 0.045 0.126 660 Planarity : 0.005 0.035 800 Dihedral : 4.733 14.750 700 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 9.50 % Allowed : 32.00 % Favored : 58.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.78 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 140 PHE 0.008 0.002 PHE P 141 TYR 0.015 0.003 TYR B 128 ARG 0.006 0.001 ARG R 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 236 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7217 (pp) REVERT: K 110 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7119 (mtpt) REVERT: K 140 HIS cc_start: 0.7007 (m170) cc_final: 0.6782 (m-70) REVERT: C 138 ILE cc_start: 0.6448 (OUTLIER) cc_final: 0.6179 (pp) REVERT: L 109 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.6379 (tmt) REVERT: L 138 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.6054 (tp) REVERT: L 140 HIS cc_start: 0.7322 (m90) cc_final: 0.6947 (m-70) REVERT: D 138 ILE cc_start: 0.7756 (mt) cc_final: 0.7494 (pp) REVERT: D 140 HIS cc_start: 0.7339 (m90) cc_final: 0.6682 (m-70) REVERT: M 140 HIS cc_start: 0.7424 (m90) cc_final: 0.6824 (m-70) REVERT: E 140 HIS cc_start: 0.7432 (m90) cc_final: 0.6995 (m-70) REVERT: I 109 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7305 (ttm) REVERT: N 109 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.5461 (tmt) REVERT: N 140 HIS cc_start: 0.7463 (m90) cc_final: 0.7055 (m-70) REVERT: S 109 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7281 (ttm) REVERT: J 109 MET cc_start: 0.7702 (mtt) cc_final: 0.7458 (mtp) REVERT: T 109 MET cc_start: 0.7665 (mtt) cc_final: 0.7401 (mtp) outliers start: 38 outliers final: 18 residues processed: 201 average time/residue: 0.9850 time to fit residues: 206.3979 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 : 0.495 ------------------------------------------------------------------------------- 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 110 LYS Chi-restraints excluded: chain P residue 122 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 D residue 125 LEU Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 129 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain S residue 134 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain J residue 134 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: 8.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.223304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.146856 restraints weight = 3583.711| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.38 r_work: 0.3977 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4154 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= 0.282 Angle : 0.662 6.993 6260 Z= 0.311 Chirality : 0.044 0.118 660 Planarity : 0.003 0.029 800 Dihedral : 4.021 14.890 700 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 8.00 % Allowed : 32.75 % 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: -4.66 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.16), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 140 PHE 0.002 0.001 PHE F 141 TYR 0.012 0.001 TYR T 128 ARG 0.005 0.001 ARG B 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 220 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7303 (pp) REVERT: K 138 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7219 (pp) REVERT: K 140 HIS cc_start: 0.6978 (m170) cc_final: 0.6694 (m-70) REVERT: P 111 HIS cc_start: 0.7769 (t70) cc_final: 0.7550 (t-90) REVERT: C 138 ILE cc_start: 0.6336 (OUTLIER) cc_final: 0.6045 (tp) REVERT: G 111 HIS cc_start: 0.7704 (t70) cc_final: 0.7375 (t-90) REVERT: L 138 ILE cc_start: 0.6388 (OUTLIER) cc_final: 0.6032 (tp) REVERT: L 140 HIS cc_start: 0.7253 (m90) cc_final: 0.6891 (m-70) REVERT: Q 111 HIS cc_start: 0.7678 (t70) cc_final: 0.7356 (t-90) REVERT: D 134 MET cc_start: 0.6888 (ttm) cc_final: 0.6662 (mmm) REVERT: D 140 HIS cc_start: 0.7308 (m90) cc_final: 0.6552 (m-70) REVERT: M 134 MET cc_start: 0.6920 (ttm) cc_final: 0.6632 (mmm) REVERT: M 140 HIS cc_start: 0.7420 (m90) cc_final: 0.6827 (m-70) REVERT: E 129 MET cc_start: 0.9028 (ttt) cc_final: 0.8449 (ttt) REVERT: E 140 HIS cc_start: 0.7434 (m90) cc_final: 0.7047 (m-70) REVERT: I 109 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7290 (ttm) REVERT: N 109 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.5415 (tmt) REVERT: N 140 HIS cc_start: 0.7490 (m90) cc_final: 0.7092 (m-70) REVERT: S 109 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7333 (ttm) REVERT: J 122 VAL cc_start: 0.7215 (p) cc_final: 0.6963 (t) REVERT: O 140 HIS cc_start: 0.7156 (m-70) cc_final: 0.6593 (m90) outliers start: 32 outliers final: 7 residues processed: 193 average time/residue: 1.0315 time to fit residues: 207.0848 Evaluate side-chains 198 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 138 ILE Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain S residue 109 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: 0.5980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 111 HIS S 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.217942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.142491 restraints weight = 3666.756| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.92 r_work: 0.3966 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 4700 Z= 0.417 Angle : 0.720 7.106 6260 Z= 0.338 Chirality : 0.043 0.117 660 Planarity : 0.005 0.046 800 Dihedral : 4.343 15.449 700 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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: -4.67 (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 0.002 0.001 HIS T 140 PHE 0.005 0.001 PHE Q 141 TYR 0.011 0.002 TYR E 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 220 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.5859 (tmt) REVERT: A 138 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7246 (pp) REVERT: K 138 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7125 (pp) REVERT: K 140 HIS cc_start: 0.6915 (m170) cc_final: 0.6616 (m-70) REVERT: P 111 HIS cc_start: 0.7779 (t70) cc_final: 0.7553 (t-90) REVERT: C 138 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.6032 (tp) REVERT: L 138 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.5913 (tp) REVERT: L 140 HIS cc_start: 0.7239 (m90) cc_final: 0.6856 (m-70) REVERT: D 134 MET cc_start: 0.7008 (ttm) cc_final: 0.6693 (mmm) REVERT: D 140 HIS cc_start: 0.7279 (m90) cc_final: 0.6538 (m-70) REVERT: M 134 MET cc_start: 0.6920 (ttm) cc_final: 0.6633 (mmm) REVERT: M 140 HIS cc_start: 0.7374 (m90) cc_final: 0.6751 (m-70) REVERT: E 129 MET cc_start: 0.8953 (ttt) cc_final: 0.8486 (ttt) REVERT: E 140 HIS cc_start: 0.7304 (m90) cc_final: 0.6899 (m-70) REVERT: I 109 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7269 (ttm) REVERT: N 109 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.5299 (tmt) REVERT: N 140 HIS cc_start: 0.7429 (m90) cc_final: 0.7012 (m-70) REVERT: S 109 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7302 (ttm) REVERT: J 109 MET cc_start: 0.7670 (mtt) cc_final: 0.7426 (mtp) REVERT: O 140 HIS cc_start: 0.7079 (m-70) cc_final: 0.6522 (m90) REVERT: T 109 MET cc_start: 0.7700 (mtt) cc_final: 0.7436 (mtp) outliers start: 29 outliers final: 14 residues processed: 194 average time/residue: 1.0010 time to fit residues: 202.2592 Evaluate side-chains 211 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain R residue 108 ASN Chi-restraints excluded: chain R residue 134 MET Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 125 LEU 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: 1.9990 chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 111 HIS S 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.217492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.140820 restraints weight = 3646.161| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.36 r_work: 0.3933 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 4700 Z= 0.438 Angle : 0.750 7.888 6260 Z= 0.350 Chirality : 0.044 0.117 660 Planarity : 0.005 0.050 800 Dihedral : 4.470 15.260 700 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.75 % Allowed : 34.50 % 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: -4.69 (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 J 140 PHE 0.005 0.001 PHE Q 141 TYR 0.013 0.002 TYR M 128 ARG 0.009 0.002 ARG B 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 217 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.5804 (tmt) REVERT: A 138 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7323 (pp) REVERT: B 111 HIS cc_start: 0.7555 (t-90) cc_final: 0.7176 (t-90) REVERT: K 138 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7219 (pp) REVERT: K 140 HIS cc_start: 0.6952 (m170) cc_final: 0.6643 (m-70) REVERT: P 111 HIS cc_start: 0.7773 (t70) cc_final: 0.7542 (t-90) REVERT: C 138 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5884 (pp) REVERT: L 140 HIS cc_start: 0.7352 (m90) cc_final: 0.7093 (m-70) REVERT: D 134 MET cc_start: 0.6984 (ttm) cc_final: 0.6692 (mmm) REVERT: D 140 HIS cc_start: 0.7353 (m90) cc_final: 0.6571 (m-70) REVERT: M 134 MET cc_start: 0.6845 (ttm) cc_final: 0.6645 (mmm) REVERT: M 140 HIS cc_start: 0.7422 (m90) cc_final: 0.6769 (m-70) REVERT: E 129 MET cc_start: 0.8951 (ttt) cc_final: 0.8746 (ttt) REVERT: E 140 HIS cc_start: 0.7354 (m90) cc_final: 0.6975 (m-70) REVERT: I 109 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7282 (ttm) REVERT: N 109 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.5351 (tmt) REVERT: N 140 HIS cc_start: 0.7480 (m90) cc_final: 0.7062 (m-70) REVERT: S 109 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7339 (ttm) REVERT: F 109 MET cc_start: 0.7431 (tpt) cc_final: 0.7155 (tpt) REVERT: J 109 MET cc_start: 0.7690 (mtt) cc_final: 0.7397 (mtp) REVERT: O 140 HIS cc_start: 0.7154 (m-70) cc_final: 0.6613 (m90) REVERT: T 109 MET cc_start: 0.7745 (mtt) cc_final: 0.7517 (mtp) outliers start: 27 outliers final: 12 residues processed: 195 average time/residue: 0.9840 time to fit residues: 199.7768 Evaluate side-chains 209 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain L residue 125 LEU 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 125 LEU Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain S residue 109 MET Chi-restraints excluded: chain 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1142 > 50: distance: 148 - 273: 13.419 distance: 158 - 276: 23.720 distance: 224 - 226: 19.893 distance: 226 - 227: 15.588 distance: 227 - 228: 27.550 distance: 228 - 229: 26.643 distance: 228 - 230: 44.209 distance: 230 - 231: 11.159 distance: 231 - 232: 10.787 distance: 231 - 234: 40.858 distance: 232 - 233: 26.709 distance: 232 - 242: 23.102 distance: 234 - 235: 11.186 distance: 235 - 236: 33.423 distance: 235 - 237: 23.336 distance: 236 - 238: 27.279 distance: 237 - 239: 28.381 distance: 238 - 240: 24.593 distance: 239 - 240: 24.515 distance: 240 - 241: 24.986 distance: 242 - 243: 36.898 distance: 243 - 244: 33.984 distance: 243 - 246: 24.038 distance: 244 - 245: 24.077 distance: 244 - 250: 12.241 distance: 246 - 247: 14.395 distance: 247 - 248: 46.442 distance: 248 - 249: 25.685 distance: 250 - 251: 22.377 distance: 251 - 252: 15.376 distance: 251 - 254: 21.452 distance: 252 - 253: 50.170 distance: 252 - 258: 6.968 distance: 255 - 256: 13.921 distance: 255 - 257: 35.716 distance: 258 - 259: 40.138 distance: 259 - 260: 50.014 distance: 260 - 261: 39.920 distance: 260 - 262: 37.968 distance: 262 - 263: 20.030 distance: 263 - 264: 23.316 distance: 263 - 266: 25.670 distance: 264 - 265: 37.492 distance: 264 - 268: 18.113 distance: 266 - 267: 21.410 distance: 268 - 269: 9.933 distance: 269 - 270: 26.314 distance: 269 - 272: 21.996 distance: 270 - 271: 13.751 distance: 270 - 273: 16.029 distance: 273 - 274: 13.184 distance: 274 - 275: 22.787 distance: 274 - 277: 35.223 distance: 275 - 276: 26.723 distance: 275 - 281: 29.408 distance: 277 - 278: 13.684 distance: 278 - 279: 19.376 distance: 279 - 280: 32.930 distance: 281 - 282: 14.447 distance: 282 - 283: 13.514 distance: 282 - 285: 38.324 distance: 283 - 284: 23.770 distance: 283 - 287: 9.446 distance: 285 - 286: 5.154 distance: 287 - 288: 6.429 distance: 288 - 289: 8.004 distance: 288 - 291: 9.136 distance: 289 - 290: 14.061 distance: 289 - 298: 18.250 distance: 291 - 292: 15.172 distance: 292 - 293: 13.952 distance: 293 - 294: 5.188 distance: 294 - 295: 18.688 distance: 295 - 296: 11.088 distance: 295 - 297: 11.356