Starting phenix.real_space_refine on Tue Jan 14 20:58:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.map" model { file = "/net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.cif" } resolution = 3.35 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= 0.015 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 32 5.16 5 C 4810 2.51 5 N 1219 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7404 Number of models: 1 Model: "" Number of chains: 15 Chain: "G" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "I" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 304 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "E" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 365 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain: "C" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 377 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "A" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2207 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 277} Chain: "H" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "J" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 304 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "F" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 365 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 377 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "B" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2207 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 277} Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.10, per 1000 atoms: 0.69 Number of scatterers: 7404 At special positions: 0 Unit cell: (94.581, 133.083, 95.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 5 15.00 O 1338 8.00 N 1219 7.00 C 4810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 256 " distance=2.04 Simple disulfide: pdb=" SG CYS B 70 " - pdb=" SG CYS B 256 " distance=2.04 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: 1.94 Conformation dependent library (CDL) restraints added in 992.6 milliseconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 34.8% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'G' and resid 7 through 16 removed outlier: 4.078A pdb=" N SER G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 14 " --> pdb=" O ILE G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 41 Processing helix chain 'I' and resid 11 through 45 removed outlier: 4.114A pdb=" N GLN I 15 " --> pdb=" O PRO I 11 " (cutoff:3.500A) Proline residue: I 40 - end of helix Processing helix chain 'E' and resid 10 through 38 removed outlier: 4.304A pdb=" N GLY E 16 " --> pdb=" O GLY E 12 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL E 27 " --> pdb=" O HIS E 23 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'C' and resid 78 through 104 Processing helix chain 'C' and resid 104 through 123 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'H' and resid 8 through 16 removed outlier: 3.989A pdb=" N SER H 13 " --> pdb=" O SER H 9 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE H 14 " --> pdb=" O ILE H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 41 Processing helix chain 'J' and resid 11 through 45 removed outlier: 4.133A pdb=" N GLN J 15 " --> pdb=" O PRO J 11 " (cutoff:3.500A) Proline residue: J 40 - end of helix Processing helix chain 'F' and resid 10 through 38 removed outlier: 4.321A pdb=" N GLY F 16 " --> pdb=" O GLY F 12 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL F 27 " --> pdb=" O HIS F 23 " (cutoff:3.500A) Proline residue: F 28 - end of helix Processing helix chain 'F' and resid 47 through 52 Processing helix chain 'D' and resid 78 through 104 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'B' and resid 62 through 68 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 90 removed outlier: 6.144A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN A 161 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 90 removed outlier: 6.201A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN B 161 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL B 165 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1530 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: 2.10 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1388 1.33 - 1.45: 1907 1.45 - 1.58: 4206 1.58 - 1.70: 10 1.70 - 1.83: 54 Bond restraints: 7565 Sorted by residual: bond pdb=" CG LEU A 295 " pdb=" CD1 LEU A 295 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.38e-01 bond pdb=" CG LEU A 311 " pdb=" CD2 LEU A 311 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.92e-01 bond pdb=" CG LEU B 295 " pdb=" CD1 LEU B 295 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.70e-01 bond pdb=" CB GLU B 270 " pdb=" CG GLU B 270 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.68e-01 bond pdb=" CG LEU B 311 " pdb=" CD2 LEU B 311 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.46e-01 ... (remaining 7560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 9847 1.48 - 2.96: 312 2.96 - 4.44: 47 4.44 - 5.93: 14 5.93 - 7.41: 1 Bond angle restraints: 10221 Sorted by residual: angle pdb=" N PHE G 40 " pdb=" CA PHE G 40 " pdb=" C PHE G 40 " ideal model delta sigma weight residual 112.87 117.03 -4.16 1.20e+00 6.94e-01 1.20e+01 angle pdb=" N GLY A 309 " pdb=" CA GLY A 309 " pdb=" C GLY A 309 " ideal model delta sigma weight residual 113.18 107.72 5.46 2.37e+00 1.78e-01 5.30e+00 angle pdb=" N TRP F 24 " pdb=" CA TRP F 24 " pdb=" C TRP F 24 " ideal model delta sigma weight residual 112.23 115.12 -2.89 1.26e+00 6.30e-01 5.26e+00 angle pdb=" N SER B 122 " pdb=" CA SER B 122 " pdb=" C SER B 122 " ideal model delta sigma weight residual 109.81 114.77 -4.96 2.21e+00 2.05e-01 5.04e+00 angle pdb=" CA CYS B 256 " pdb=" CB CYS B 256 " pdb=" SG CYS B 256 " ideal model delta sigma weight residual 114.40 119.50 -5.10 2.30e+00 1.89e-01 4.92e+00 ... (remaining 10216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 4387 34.35 - 68.70: 109 68.70 - 103.04: 15 103.04 - 137.39: 10 137.39 - 171.74: 2 Dihedral angle restraints: 4523 sinusoidal: 1877 harmonic: 2646 Sorted by residual: dihedral pdb=" CA LEU B 311 " pdb=" C LEU B 311 " pdb=" N GLU B 312 " pdb=" CA GLU B 312 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TRP A 305 " pdb=" C TRP A 305 " pdb=" N GLN A 306 " pdb=" CA GLN A 306 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU A 318 " pdb=" C LEU A 318 " pdb=" N PRO A 319 " pdb=" CA PRO A 319 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 4520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1016 0.072 - 0.143: 108 0.143 - 0.215: 2 0.215 - 0.286: 0 0.286 - 0.358: 1 Chirality restraints: 1127 Sorted by residual: chirality pdb=" CA PHE G 40 " pdb=" N PHE G 40 " pdb=" C PHE G 40 " pdb=" CB PHE G 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ILE B 99 " pdb=" N ILE B 99 " pdb=" C ILE B 99 " pdb=" CB ILE B 99 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA ILE A 99 " pdb=" N ILE A 99 " pdb=" C ILE A 99 " pdb=" CB ILE A 99 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 1124 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 113 " -0.269 9.50e-02 1.11e+02 1.21e-01 1.04e+01 pdb=" NE ARG D 113 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 113 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D 113 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG D 113 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 113 " 0.246 9.50e-02 1.11e+02 1.10e-01 7.90e+00 pdb=" NE ARG C 113 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 113 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 113 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 113 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 286 " -0.005 2.00e-02 2.50e+03 1.32e-02 3.49e+00 pdb=" CG TYR B 286 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 286 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 286 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 286 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 286 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 286 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR B 286 " -0.022 2.00e-02 2.50e+03 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2732 2.88 - 3.39: 7049 3.39 - 3.89: 11692 3.89 - 4.40: 13093 4.40 - 4.90: 23915 Nonbonded interactions: 58481 Sorted by model distance: nonbonded pdb=" OH TYR A 257 " pdb=" OE1 GLN A 259 " model vdw 2.377 3.040 nonbonded pdb=" OH TYR B 257 " pdb=" OE1 GLN B 259 " model vdw 2.401 3.040 nonbonded pdb=" NH1 ARG B 110 " pdb=" OD1 ASP B 133 " model vdw 2.440 3.120 nonbonded pdb=" O VAL C 107 " pdb=" OG1 THR C 111 " model vdw 2.443 3.040 nonbonded pdb=" O2 PLC C 401 " pdb=" O3 PLC C 401 " model vdw 2.444 2.432 ... (remaining 58476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 55 through 344) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.920 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.003 0.026 7565 Z= 0.174 Angle : 0.643 7.406 10221 Z= 0.359 Chirality : 0.044 0.358 1127 Planarity : 0.007 0.121 1286 Dihedral : 17.420 171.741 2817 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.09 (0.27), residues: 908 helix: -0.30 (0.26), residues: 282 sheet: 0.55 (0.26), residues: 394 loop : -0.49 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 305 HIS 0.007 0.002 HIS B 330 PHE 0.016 0.003 PHE B 127 TYR 0.022 0.006 TYR B 286 ARG 0.021 0.003 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.835 Fit side-chains REVERT: C 115 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7667 (tm-30) REVERT: D 115 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 155 LYS cc_start: 0.7458 (mttp) cc_final: 0.7038 (mtpt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1856 time to fit residues: 47.9643 Evaluate side-chains 130 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.0010 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS J 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.220142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.184370 restraints weight = 9351.059| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 2.70 r_work: 0.4272 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7565 Z= 0.248 Angle : 0.746 14.542 10221 Z= 0.387 Chirality : 0.048 0.197 1127 Planarity : 0.005 0.041 1286 Dihedral : 16.912 168.371 1171 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.97 % Allowed : 9.17 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.76 (0.28), residues: 908 helix: 1.24 (0.29), residues: 288 sheet: 0.37 (0.25), residues: 394 loop : 0.06 (0.48), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 244 HIS 0.004 0.001 HIS B 254 PHE 0.022 0.002 PHE I 29 TYR 0.016 0.002 TYR F 32 ARG 0.003 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.786 Fit side-chains REVERT: C 108 ILE cc_start: 0.8031 (mt) cc_final: 0.7804 (tp) REVERT: C 115 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 141 ASN cc_start: 0.8768 (m110) cc_final: 0.8559 (m-40) REVERT: A 298 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.6722 (mtm-85) REVERT: A 342 MET cc_start: 0.7645 (ttp) cc_final: 0.7390 (tpp) REVERT: D 91 ASN cc_start: 0.6168 (m-40) cc_final: 0.5966 (t0) REVERT: D 108 ILE cc_start: 0.8062 (mt) cc_final: 0.7801 (tp) REVERT: D 115 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 155 LYS cc_start: 0.7480 (mttp) cc_final: 0.6968 (mtpt) REVERT: B 298 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.6757 (mtm-85) outliers start: 23 outliers final: 16 residues processed: 158 average time/residue: 0.1882 time to fit residues: 40.3935 Evaluate side-chains 144 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 70 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 HIS A 254 HIS D 120 HIS B 254 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.220761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.182988 restraints weight = 9156.521| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 2.71 r_work: 0.4272 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7565 Z= 0.223 Angle : 0.687 10.808 10221 Z= 0.353 Chirality : 0.046 0.193 1127 Planarity : 0.004 0.043 1286 Dihedral : 15.954 165.893 1171 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.97 % Allowed : 11.63 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.90 (0.28), residues: 908 helix: 1.45 (0.28), residues: 298 sheet: 0.40 (0.26), residues: 392 loop : 0.04 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 94 HIS 0.004 0.001 HIS C 120 PHE 0.015 0.002 PHE I 29 TYR 0.015 0.001 TYR B 115 ARG 0.002 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.857 Fit side-chains REVERT: I 7 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8388 (p) REVERT: C 115 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7861 (tm-30) REVERT: J 7 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8334 (p) REVERT: D 115 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 231 MET cc_start: 0.7436 (tpt) cc_final: 0.7221 (tpt) REVERT: B 298 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.6622 (mtm-85) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 0.1901 time to fit residues: 37.5579 Evaluate side-chains 141 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 HIS B 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.219508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.181428 restraints weight = 9086.611| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 2.71 r_work: 0.4258 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7565 Z= 0.232 Angle : 0.678 10.914 10221 Z= 0.350 Chirality : 0.046 0.195 1127 Planarity : 0.004 0.045 1286 Dihedral : 15.461 164.720 1171 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.71 % Allowed : 13.70 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.04 (0.29), residues: 908 helix: 1.63 (0.29), residues: 298 sheet: 0.43 (0.26), residues: 392 loop : 0.11 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 94 HIS 0.005 0.001 HIS B 146 PHE 0.021 0.002 PHE D 109 TYR 0.017 0.002 TYR A 115 ARG 0.005 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.706 Fit side-chains REVERT: C 108 ILE cc_start: 0.7954 (mt) cc_final: 0.7725 (tp) REVERT: C 115 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7832 (tm-30) REVERT: D 115 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7788 (tm-30) outliers start: 21 outliers final: 19 residues processed: 141 average time/residue: 0.1818 time to fit residues: 35.3509 Evaluate side-chains 145 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.217304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.179536 restraints weight = 9089.776| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 2.66 r_work: 0.4245 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7565 Z= 0.253 Angle : 0.695 10.958 10221 Z= 0.352 Chirality : 0.045 0.171 1127 Planarity : 0.004 0.046 1286 Dihedral : 15.273 164.196 1171 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.10 % Allowed : 14.73 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.04 (0.29), residues: 908 helix: 1.63 (0.28), residues: 310 sheet: 0.43 (0.26), residues: 392 loop : 0.02 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 94 HIS 0.006 0.001 HIS A 146 PHE 0.022 0.002 PHE D 109 TYR 0.019 0.002 TYR B 115 ARG 0.003 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.689 Fit side-chains REVERT: I 7 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8369 (p) REVERT: C 115 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 155 LYS cc_start: 0.7415 (mttp) cc_final: 0.6967 (mtpt) REVERT: J 7 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8394 (p) outliers start: 24 outliers final: 19 residues processed: 137 average time/residue: 0.1789 time to fit residues: 33.5919 Evaluate side-chains 140 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4735 r_free = 0.4735 target = 0.215818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.177982 restraints weight = 9115.327| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 2.65 r_work: 0.4224 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7565 Z= 0.275 Angle : 0.722 11.343 10221 Z= 0.363 Chirality : 0.045 0.168 1127 Planarity : 0.004 0.045 1286 Dihedral : 15.324 163.939 1171 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.88 % Allowed : 15.63 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.98 (0.29), residues: 908 helix: 1.72 (0.28), residues: 310 sheet: 0.30 (0.26), residues: 394 loop : -0.02 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 94 HIS 0.004 0.001 HIS F 23 PHE 0.023 0.002 PHE D 109 TYR 0.020 0.002 TYR B 115 ARG 0.003 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.860 Fit side-chains REVERT: I 7 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8419 (p) REVERT: A 155 LYS cc_start: 0.7418 (mttp) cc_final: 0.6955 (mtpt) REVERT: A 342 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7286 (ttp) REVERT: D 115 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 231 MET cc_start: 0.7288 (tpt) cc_final: 0.6918 (tpt) outliers start: 30 outliers final: 22 residues processed: 140 average time/residue: 0.1762 time to fit residues: 34.4485 Evaluate side-chains 147 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 26 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4702 r_free = 0.4702 target = 0.211510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.172955 restraints weight = 9192.723| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.70 r_work: 0.4171 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7565 Z= 0.401 Angle : 0.811 12.043 10221 Z= 0.407 Chirality : 0.048 0.176 1127 Planarity : 0.005 0.045 1286 Dihedral : 15.452 163.728 1171 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.75 % Allowed : 17.31 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.65 (0.29), residues: 908 helix: 1.50 (0.28), residues: 310 sheet: 0.13 (0.26), residues: 388 loop : -0.32 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 53 HIS 0.004 0.002 HIS B 97 PHE 0.017 0.002 PHE B 148 TYR 0.021 0.003 TYR A 115 ARG 0.003 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.780 Fit side-chains REVERT: C 115 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7771 (tm-30) REVERT: A 155 LYS cc_start: 0.7483 (mttp) cc_final: 0.7003 (mtpt) REVERT: A 342 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7352 (ttp) REVERT: B 298 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.6666 (mtm-85) outliers start: 29 outliers final: 22 residues processed: 139 average time/residue: 0.1690 time to fit residues: 33.1691 Evaluate side-chains 146 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.0000 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.4772 r_free = 0.4772 target = 0.219079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.182057 restraints weight = 9188.743| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 2.68 r_work: 0.4257 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7565 Z= 0.198 Angle : 0.696 12.439 10221 Z= 0.346 Chirality : 0.045 0.156 1127 Planarity : 0.004 0.046 1286 Dihedral : 14.764 164.744 1171 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.84 % Allowed : 17.96 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.06 (0.29), residues: 908 helix: 1.94 (0.29), residues: 310 sheet: 0.21 (0.27), residues: 394 loop : 0.04 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 94 HIS 0.006 0.001 HIS F 23 PHE 0.024 0.002 PHE C 109 TYR 0.024 0.001 TYR B 115 ARG 0.002 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.863 Fit side-chains REVERT: C 115 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 342 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7161 (ttp) REVERT: D 115 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7644 (tm-30) REVERT: D 116 MET cc_start: 0.7648 (tpp) cc_final: 0.7419 (tpp) REVERT: B 64 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 68 LYS cc_start: 0.6687 (ttpt) cc_final: 0.6429 (ttmm) REVERT: B 231 MET cc_start: 0.7064 (tpt) cc_final: 0.6687 (tpt) outliers start: 22 outliers final: 17 residues processed: 149 average time/residue: 0.1771 time to fit residues: 36.3679 Evaluate side-chains 141 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.215547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.177958 restraints weight = 9165.728| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.69 r_work: 0.4231 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7565 Z= 0.249 Angle : 0.735 13.052 10221 Z= 0.366 Chirality : 0.045 0.168 1127 Planarity : 0.004 0.046 1286 Dihedral : 14.527 162.703 1171 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.23 % Allowed : 18.22 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.14 (0.29), residues: 908 helix: 2.00 (0.29), residues: 310 sheet: 0.34 (0.27), residues: 388 loop : -0.07 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 94 HIS 0.005 0.001 HIS F 23 PHE 0.019 0.002 PHE J 29 TYR 0.021 0.002 TYR B 115 ARG 0.003 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.826 Fit side-chains REVERT: C 115 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 155 LYS cc_start: 0.7430 (mttp) cc_final: 0.6980 (mtpt) REVERT: D 115 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7557 (tm-30) REVERT: D 116 MET cc_start: 0.7712 (tpp) cc_final: 0.7475 (tpp) REVERT: B 68 LYS cc_start: 0.6630 (ttpt) cc_final: 0.6402 (ttmm) REVERT: B 231 MET cc_start: 0.7299 (tpt) cc_final: 0.7003 (tpp) outliers start: 25 outliers final: 21 residues processed: 137 average time/residue: 0.1718 time to fit residues: 32.7464 Evaluate side-chains 140 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 67 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.216405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.178923 restraints weight = 9223.750| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.70 r_work: 0.4248 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7565 Z= 0.227 Angle : 0.735 13.499 10221 Z= 0.363 Chirality : 0.045 0.165 1127 Planarity : 0.004 0.046 1286 Dihedral : 14.239 161.997 1171 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.84 % Allowed : 18.86 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.22 (0.29), residues: 908 helix: 2.11 (0.29), residues: 310 sheet: 0.31 (0.27), residues: 392 loop : 0.03 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 94 HIS 0.005 0.001 HIS F 23 PHE 0.027 0.002 PHE C 109 TYR 0.021 0.002 TYR B 115 ARG 0.003 0.000 ARG B 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.781 Fit side-chains REVERT: G 46 MET cc_start: 0.7928 (ptm) cc_final: 0.7717 (ptp) REVERT: C 115 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7674 (tm-30) REVERT: C 116 MET cc_start: 0.7675 (tpt) cc_final: 0.7473 (tpp) REVERT: A 155 LYS cc_start: 0.7426 (mttp) cc_final: 0.6985 (mtpt) REVERT: D 116 MET cc_start: 0.7693 (tpp) cc_final: 0.7492 (tpp) REVERT: B 68 LYS cc_start: 0.6623 (ttpt) cc_final: 0.6392 (ttmm) outliers start: 22 outliers final: 21 residues processed: 133 average time/residue: 0.1763 time to fit residues: 32.5677 Evaluate side-chains 142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4751 r_free = 0.4751 target = 0.218216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.180420 restraints weight = 9126.823| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 2.68 r_work: 0.4240 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7565 Z= 0.238 Angle : 0.741 13.194 10221 Z= 0.367 Chirality : 0.045 0.170 1127 Planarity : 0.004 0.045 1286 Dihedral : 14.024 161.001 1171 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.10 % Allowed : 18.60 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.24 (0.29), residues: 908 helix: 2.14 (0.29), residues: 310 sheet: 0.31 (0.27), residues: 392 loop : 0.03 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 94 HIS 0.005 0.001 HIS F 23 PHE 0.030 0.002 PHE D 109 TYR 0.020 0.002 TYR B 115 ARG 0.003 0.000 ARG B 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.83 seconds wall clock time: 62 minutes 55.64 seconds (3775.64 seconds total)