Starting phenix.real_space_refine on Wed Mar 12 06:03:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9etm_19944/03_2025/9etm_19944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9etm_19944/03_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_19944/03_2025/9etm_19944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9etm_19944/03_2025/9etm_19944.map" model { file = "/net/cci-nas-00/data/ceres_data/9etm_19944/03_2025/9etm_19944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9etm_19944/03_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-5624/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: 5.22, per 1000 atoms: 0.71 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: 1.67 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.63 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: 2.24 Time building geometry restraints manager: 1.99 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: 3.180 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.040 Find NCS groups from input model: 0.280 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.000 ------------------------------------------------------------------------------- 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 : 0.722 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: 0.1804 time to fit residues: 46.3980 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 : 0.781 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.184451 restraints weight = 9351.064| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 2.69 r_work: 0.4273 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 : 0.828 Fit side-chains REVERT: C 108 ILE cc_start: 0.8030 (mt) cc_final: 0.7803 (tp) REVERT: C 115 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 141 ASN cc_start: 0.8768 (m110) cc_final: 0.8558 (m-40) REVERT: A 298 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.6720 (mtm-85) REVERT: A 342 MET cc_start: 0.7644 (ttp) cc_final: 0.7390 (tpp) REVERT: D 91 ASN cc_start: 0.6165 (m-40) cc_final: 0.5963 (t0) REVERT: D 108 ILE cc_start: 0.8062 (mt) cc_final: 0.7802 (tp) REVERT: D 115 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 155 LYS cc_start: 0.7478 (mttp) cc_final: 0.6966 (mtpt) REVERT: B 298 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.6756 (mtm-85) outliers start: 23 outliers final: 16 residues processed: 158 average time/residue: 0.1843 time to fit residues: 39.5752 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 : 0.747 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 8 GLN C 120 HIS A 254 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 = 0.4764 r_free = 0.4764 target = 0.219466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.182015 restraints weight = 9150.517| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 2.67 r_work: 0.4264 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7565 Z= 0.228 Angle : 0.687 10.485 10221 Z= 0.354 Chirality : 0.046 0.195 1127 Planarity : 0.004 0.043 1286 Dihedral : 15.955 165.630 1171 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.71 % Allowed : 11.76 % Favored : 85.53 % 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: 0.87 (0.28), residues: 908 helix: 1.43 (0.28), residues: 298 sheet: 0.38 (0.26), residues: 392 loop : 0.03 (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 0.002 TYR B 115 ARG 0.002 0.000 ARG B 336 *********************** 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 159 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.741 Fit side-chains REVERT: I 7 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8453 (p) REVERT: C 115 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7935 (tm-30) REVERT: J 7 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8431 (p) REVERT: D 115 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 231 MET cc_start: 0.7428 (tpt) cc_final: 0.7199 (tpt) REVERT: B 298 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.6662 (mtm-85) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 0.1815 time to fit residues: 35.9144 Evaluate side-chains 138 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 4 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 HIS B 97 HIS B 146 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.218296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.180449 restraints weight = 9109.939| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 2.69 r_work: 0.4246 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2924 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= 0.244 Angle : 0.694 11.157 10221 Z= 0.354 Chirality : 0.046 0.191 1127 Planarity : 0.004 0.045 1286 Dihedral : 15.614 164.180 1171 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.10 % Allowed : 13.44 % Favored : 83.46 % 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: 0.92 (0.29), residues: 908 helix: 1.52 (0.28), residues: 308 sheet: 0.39 (0.26), residues: 392 loop : -0.06 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 94 HIS 0.005 0.002 HIS B 146 PHE 0.021 0.002 PHE C 109 TYR 0.018 0.002 TYR A 115 ARG 0.003 0.000 ARG B 110 *********************** 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 152 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.755 Fit side-chains REVERT: I 7 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8346 (p) REVERT: C 108 ILE cc_start: 0.7971 (mt) cc_final: 0.7756 (tp) REVERT: C 115 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7811 (tm-30) REVERT: J 7 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8356 (p) REVERT: D 115 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7754 (tm-30) REVERT: D 116 MET cc_start: 0.7505 (tpp) cc_final: 0.7296 (tpt) outliers start: 24 outliers final: 20 residues processed: 139 average time/residue: 0.1732 time to fit residues: 33.2470 Evaluate side-chains 142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 223 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.215816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.177967 restraints weight = 9127.262| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 2.66 r_work: 0.4223 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7565 Z= 0.280 Angle : 0.707 10.535 10221 Z= 0.360 Chirality : 0.046 0.183 1127 Planarity : 0.004 0.045 1286 Dihedral : 15.502 164.050 1171 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.26 % Allowed : 14.47 % Favored : 81.27 % 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: 0.88 (0.29), residues: 908 helix: 1.59 (0.28), residues: 310 sheet: 0.30 (0.26), residues: 394 loop : -0.13 (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 0.022 0.002 PHE C 109 TYR 0.018 0.002 TYR B 115 ARG 0.004 0.000 ARG A 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 155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.817 Fit side-chains REVERT: I 7 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8414 (p) REVERT: C 115 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7759 (tm-30) REVERT: A 155 LYS cc_start: 0.7415 (mttp) cc_final: 0.6950 (mtpt) REVERT: A 342 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7334 (ttp) REVERT: D 115 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7697 (tm-30) outliers start: 33 outliers final: 25 residues processed: 138 average time/residue: 0.1777 time to fit residues: 33.5284 Evaluate side-chains 147 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 MET 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 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 110 ARG 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 D residue 119 LEU 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: 2.9990 chunk 51 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4753 r_free = 0.4753 target = 0.217306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.179663 restraints weight = 9141.025| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.69 r_work: 0.4248 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7565 Z= 0.212 Angle : 0.685 11.206 10221 Z= 0.342 Chirality : 0.045 0.154 1127 Planarity : 0.004 0.045 1286 Dihedral : 14.991 164.247 1171 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.36 % Allowed : 16.67 % Favored : 79.97 % 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: 1.08 (0.29), residues: 908 helix: 1.81 (0.29), residues: 310 sheet: 0.33 (0.27), residues: 394 loop : 0.04 (0.48), residues: 204 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 0.022 0.002 PHE D 109 TYR 0.020 0.001 TYR B 115 ARG 0.002 0.000 ARG B 110 *********************** 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 162 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.808 Fit side-chains REVERT: A 68 LYS cc_start: 0.6708 (ttpt) cc_final: 0.6483 (ttmm) REVERT: A 155 LYS cc_start: 0.7383 (mttp) cc_final: 0.6920 (mtpt) REVERT: B 231 MET cc_start: 0.7188 (tpt) cc_final: 0.6874 (tpt) REVERT: B 247 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7624 (t) outliers start: 26 outliers final: 20 residues processed: 149 average time/residue: 0.1892 time to fit residues: 38.4617 Evaluate side-chains 145 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 110 ARG 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 223 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 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: 0.9990 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 28 optimal weight: 0.0030 overall best weight: 1.5996 ------------------------------------------------------------------------------- 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 = 0.4712 r_free = 0.4712 target = 0.212446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.174376 restraints weight = 9155.884| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.66 r_work: 0.4194 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7565 Z= 0.338 Angle : 0.777 11.975 10221 Z= 0.388 Chirality : 0.047 0.172 1127 Planarity : 0.005 0.045 1286 Dihedral : 15.059 163.327 1171 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.88 % Allowed : 17.44 % Favored : 78.68 % 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: 0.86 (0.29), residues: 908 helix: 1.72 (0.28), residues: 310 sheet: 0.23 (0.27), residues: 388 loop : -0.27 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 53 HIS 0.005 0.001 HIS B 97 PHE 0.035 0.002 PHE J 29 TYR 0.021 0.003 TYR B 115 ARG 0.004 0.000 ARG A 110 *********************** 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 163 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.826 Fit side-chains REVERT: C 115 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 155 LYS cc_start: 0.7446 (mttp) cc_final: 0.6984 (mtpt) REVERT: D 115 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 155 LYS cc_start: 0.7594 (mttp) cc_final: 0.7132 (mtpt) REVERT: B 298 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7298 (mtm-85) outliers start: 30 outliers final: 25 residues processed: 146 average time/residue: 0.1747 time to fit residues: 35.2042 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 : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 MET 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 110 ARG 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 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain H residue 22 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 152 LEU Chi-restraints excluded: chain B residue 172 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: 4.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 52 optimal weight: 0.0020 chunk 9 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.4750 r_free = 0.4750 target = 0.219567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.183972 restraints weight = 9608.378| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 2.75 r_work: 0.4261 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7565 Z= 0.196 Angle : 0.693 12.691 10221 Z= 0.344 Chirality : 0.045 0.155 1127 Planarity : 0.004 0.045 1286 Dihedral : 14.451 164.179 1171 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.36 % Allowed : 17.70 % 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: 1.16 (0.29), residues: 908 helix: 2.05 (0.29), residues: 310 sheet: 0.25 (0.27), residues: 394 loop : 0.09 (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 0.001 PHE C 109 TYR 0.023 0.001 TYR A 115 ARG 0.002 0.000 ARG B 336 *********************** 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 155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.854 Fit side-chains REVERT: C 115 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7741 (tm-30) REVERT: A 155 LYS cc_start: 0.7398 (mttp) cc_final: 0.6946 (mtpt) REVERT: D 115 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 247 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7592 (t) outliers start: 26 outliers final: 18 residues processed: 139 average time/residue: 0.1754 time to fit residues: 33.5248 Evaluate side-chains 140 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain H residue 22 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 247 THR 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: 0.5980 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.215741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.178203 restraints weight = 9178.110| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.68 r_work: 0.4232 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3979 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= 0.242 Angle : 0.728 12.829 10221 Z= 0.362 Chirality : 0.045 0.174 1127 Planarity : 0.004 0.046 1286 Dihedral : 14.339 161.890 1171 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.17 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: 1.18 (0.29), residues: 908 helix: 2.11 (0.29), residues: 310 sheet: 0.32 (0.27), residues: 384 loop : -0.11 (0.46), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 305 HIS 0.007 0.002 HIS A 146 PHE 0.025 0.002 PHE D 109 TYR 0.022 0.002 TYR A 115 ARG 0.003 0.000 ARG A 110 *********************** 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 143 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.740 Fit side-chains REVERT: C 115 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7697 (tm-30) REVERT: A 155 LYS cc_start: 0.7484 (mttp) cc_final: 0.7046 (mtpt) REVERT: D 115 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 155 LYS cc_start: 0.7580 (mttp) cc_final: 0.7135 (mtpt) outliers start: 24 outliers final: 19 residues processed: 129 average time/residue: 0.1751 time to fit residues: 31.3961 Evaluate side-chains 134 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 MET 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 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 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain H residue 22 MET 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 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: 5.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 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 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.217132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.179712 restraints weight = 9262.098| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 2.72 r_work: 0.4247 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7565 Z= 0.221 Angle : 0.715 13.406 10221 Z= 0.354 Chirality : 0.045 0.159 1127 Planarity : 0.004 0.045 1286 Dihedral : 14.033 161.781 1171 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.45 % Allowed : 18.73 % Favored : 78.81 % 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: 2.18 (0.29), residues: 310 sheet: 0.30 (0.27), residues: 392 loop : 0.00 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 94 HIS 0.008 0.001 HIS A 146 PHE 0.027 0.001 PHE C 109 TYR 0.022 0.002 TYR A 115 ARG 0.002 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 144 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.751 Fit side-chains REVERT: C 115 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7682 (tm-30) REVERT: A 155 LYS cc_start: 0.7445 (mttp) cc_final: 0.7024 (mtpt) REVERT: D 115 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7595 (tm-30) REVERT: B 155 LYS cc_start: 0.7614 (mttp) cc_final: 0.7242 (mtpt) outliers start: 19 outliers final: 18 residues processed: 132 average time/residue: 0.1742 time to fit residues: 31.8838 Evaluate side-chains 138 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 VAL 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 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain H residue 22 MET 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: 2.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.217348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.179977 restraints weight = 9125.164| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 2.68 r_work: 0.4252 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7565 Z= 0.219 Angle : 0.725 13.078 10221 Z= 0.356 Chirality : 0.045 0.163 1127 Planarity : 0.004 0.046 1286 Dihedral : 13.688 159.984 1171 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.97 % Allowed : 18.60 % Favored : 78.42 % 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: 1.31 (0.29), residues: 908 helix: 2.20 (0.29), residues: 310 sheet: 0.34 (0.27), residues: 392 loop : 0.06 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 94 HIS 0.008 0.002 HIS A 146 PHE 0.027 0.002 PHE D 109 TYR 0.022 0.002 TYR A 115 ARG 0.002 0.000 ARG A 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3446.78 seconds wall clock time: 60 minutes 18.08 seconds (3618.08 seconds total)