Starting phenix.real_space_refine on Tue Mar 3 19:38:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ot9_13057/03_2026/7ot9_13057.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ot9_13057/03_2026/7ot9_13057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ot9_13057/03_2026/7ot9_13057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ot9_13057/03_2026/7ot9_13057.map" model { file = "/net/cci-nas-00/data/ceres_data/7ot9_13057/03_2026/7ot9_13057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ot9_13057/03_2026/7ot9_13057.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5650 2.51 5 N 1395 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8410 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Restraints were copied for chains: E, D, C, B Time building chain proxies: 0.92, per 1000 atoms: 0.11 Number of scatterers: 8410 At special positions: 0 Unit cell: (126.312, 125.204, 60.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1310 8.00 N 1395 7.00 C 5650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 324.4 milliseconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 9 through 48 Proline residue: A 33 - end of helix removed outlier: 4.468A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 167 through 180 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU A 281 " --> pdb=" O TRP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 307 through 322 Processing helix chain 'A' and resid 325 through 346 Proline residue: A 331 - end of helix Processing helix chain 'E' and resid 9 through 48 Proline residue: E 33 - end of helix removed outlier: 4.468A pdb=" N LEU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 180 through 196 Processing helix chain 'E' and resid 198 through 230 removed outlier: 3.996A pdb=" N GLY E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU E 281 " --> pdb=" O TRP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 307 through 322 Processing helix chain 'E' and resid 325 through 346 Proline residue: E 331 - end of helix Processing helix chain 'D' and resid 9 through 48 Proline residue: D 33 - end of helix removed outlier: 4.468A pdb=" N LEU D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 289 removed outlier: 3.748A pdb=" N LEU D 281 " --> pdb=" O TRP D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'D' and resid 307 through 322 Processing helix chain 'D' and resid 325 through 346 Proline residue: D 331 - end of helix Processing helix chain 'C' and resid 9 through 48 Proline residue: C 33 - end of helix removed outlier: 4.468A pdb=" N LEU C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 59 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 167 through 180 Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU C 281 " --> pdb=" O TRP C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 307 through 322 Processing helix chain 'C' and resid 325 through 346 Proline residue: C 331 - end of helix Processing helix chain 'B' and resid 9 through 48 Proline residue: B 33 - end of helix removed outlier: 4.468A pdb=" N LEU B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 62 through 79 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU B 281 " --> pdb=" O TRP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 307 through 322 Processing helix chain 'B' and resid 325 through 346 Proline residue: B 331 - end of helix 695 hydrogen bonds defined for protein. 2055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2565 1.34 - 1.46: 1319 1.46 - 1.57: 4606 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 8590 Sorted by residual: bond pdb=" C ALA C 41 " pdb=" N GLY C 42 " ideal model delta sigma weight residual 1.331 1.316 0.015 1.46e-02 4.69e+03 1.01e+00 bond pdb=" C ALA D 41 " pdb=" N GLY D 42 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.84e-01 bond pdb=" C ALA A 41 " pdb=" N GLY A 42 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.59e-01 bond pdb=" C ALA B 41 " pdb=" N GLY B 42 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 9.11e-01 bond pdb=" C ALA E 41 " pdb=" N GLY E 42 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 9.03e-01 ... (remaining 8585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 11006 1.20 - 2.40: 569 2.40 - 3.60: 85 3.60 - 4.80: 50 4.80 - 6.00: 20 Bond angle restraints: 11730 Sorted by residual: angle pdb=" N VAL E 198 " pdb=" CA VAL E 198 " pdb=" C VAL E 198 " ideal model delta sigma weight residual 113.53 108.12 5.41 9.80e-01 1.04e+00 3.05e+01 angle pdb=" N VAL B 198 " pdb=" CA VAL B 198 " pdb=" C VAL B 198 " ideal model delta sigma weight residual 113.53 108.15 5.38 9.80e-01 1.04e+00 3.01e+01 angle pdb=" N VAL C 198 " pdb=" CA VAL C 198 " pdb=" C VAL C 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.01e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.00e+01 angle pdb=" N VAL D 198 " pdb=" CA VAL D 198 " pdb=" C VAL D 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.00e+01 ... (remaining 11725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4470 17.70 - 35.40: 410 35.40 - 53.10: 45 53.10 - 70.80: 10 70.80 - 88.49: 15 Dihedral angle restraints: 4950 sinusoidal: 1845 harmonic: 3105 Sorted by residual: dihedral pdb=" CA ASN A 293 " pdb=" C ASN A 293 " pdb=" N VAL A 294 " pdb=" CA VAL A 294 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN C 293 " pdb=" C ASN C 293 " pdb=" N VAL C 294 " pdb=" CA VAL C 294 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN D 293 " pdb=" C ASN D 293 " pdb=" N VAL D 294 " pdb=" CA VAL D 294 " ideal model delta harmonic sigma weight residual 180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 4947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 840 0.031 - 0.062: 479 0.062 - 0.092: 124 0.092 - 0.123: 37 0.123 - 0.154: 10 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CB ILE E 300 " pdb=" CA ILE E 300 " pdb=" CG1 ILE E 300 " pdb=" CG2 ILE E 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB ILE A 300 " pdb=" CA ILE A 300 " pdb=" CG1 ILE A 300 " pdb=" CG2 ILE A 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CB ILE B 300 " pdb=" CA ILE B 300 " pdb=" CG1 ILE B 300 " pdb=" CG2 ILE B 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 1487 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 42 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C GLY C 42 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY C 42 " -0.015 2.00e-02 2.50e+03 pdb=" N THR C 43 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 42 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C GLY B 42 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY B 42 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 43 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 42 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C GLY D 42 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY D 42 " -0.015 2.00e-02 2.50e+03 pdb=" N THR D 43 " -0.014 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 103 2.69 - 3.24: 8869 3.24 - 3.80: 13722 3.80 - 4.35: 15471 4.35 - 4.90: 27598 Nonbonded interactions: 65763 Sorted by model distance: nonbonded pdb=" O TRP D 344 " pdb=" NH1 ARG C 194 " model vdw 2.138 3.120 nonbonded pdb=" OG1 THR C 48 " pdb=" OH TYR C 178 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR E 48 " pdb=" OH TYR E 178 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR D 48 " pdb=" OH TYR D 178 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR A 48 " pdb=" OH TYR A 178 " model vdw 2.141 3.040 ... (remaining 65758 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'D' selection = chain 'C' selection = chain 'B' } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.310 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.005 0.030 8590 Z= 0.213 Angle : 0.667 6.000 11730 Z= 0.365 Chirality : 0.040 0.154 1490 Planarity : 0.004 0.023 1385 Dihedral : 14.505 88.495 2940 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.25), residues: 1075 helix: 2.27 (0.17), residues: 905 sheet: None (None), residues: 0 loop : -2.04 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 301 TYR 0.003 0.001 TYR B 178 PHE 0.011 0.001 PHE C 163 TRP 0.007 0.001 TRP B 344 HIS 0.019 0.007 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 8590) covalent geometry : angle 0.66731 (11730) hydrogen bonds : bond 0.09765 ( 695) hydrogen bonds : angle 4.69709 ( 2055) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.319 Fit side-chains REVERT: A 170 MET cc_start: 0.6257 (ttm) cc_final: 0.5920 (ttm) REVERT: E 170 MET cc_start: 0.6847 (ttm) cc_final: 0.6643 (ttm) REVERT: E 182 GLU cc_start: 0.8133 (mp0) cc_final: 0.7813 (mp0) REVERT: E 302 MET cc_start: 0.8221 (mpp) cc_final: 0.7746 (mpt) REVERT: D 170 MET cc_start: 0.6758 (ttm) cc_final: 0.6502 (ttm) REVERT: D 182 GLU cc_start: 0.8336 (mp0) cc_final: 0.8060 (mp0) REVERT: C 178 TYR cc_start: 0.9038 (m-80) cc_final: 0.8599 (m-80) REVERT: C 182 GLU cc_start: 0.8276 (mp0) cc_final: 0.7959 (mp0) REVERT: C 302 MET cc_start: 0.7952 (mpp) cc_final: 0.7726 (mpt) REVERT: B 170 MET cc_start: 0.6627 (ttm) cc_final: 0.6325 (ttm) REVERT: B 182 GLU cc_start: 0.8352 (mp0) cc_final: 0.8080 (mp0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.6014 time to fit residues: 72.7147 Evaluate side-chains 87 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.101777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072865 restraints weight = 18477.363| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.85 r_work: 0.3014 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8590 Z= 0.137 Angle : 0.624 7.056 11730 Z= 0.307 Chirality : 0.038 0.142 1490 Planarity : 0.005 0.038 1385 Dihedral : 4.432 20.790 1155 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.91 % Allowed : 14.51 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.25), residues: 1075 helix: 2.69 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.11 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 194 TYR 0.006 0.002 TYR B 178 PHE 0.008 0.001 PHE B 163 TRP 0.007 0.001 TRP B 344 HIS 0.013 0.005 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8590) covalent geometry : angle 0.62436 (11730) hydrogen bonds : bond 0.03832 ( 695) hydrogen bonds : angle 4.08030 ( 2055) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.6397 (ttm) cc_final: 0.6188 (ttm) REVERT: A 182 GLU cc_start: 0.8644 (mp0) cc_final: 0.8322 (mp0) REVERT: E 182 GLU cc_start: 0.8694 (mp0) cc_final: 0.8298 (mp0) REVERT: E 302 MET cc_start: 0.8189 (mpp) cc_final: 0.7803 (mpt) REVERT: D 170 MET cc_start: 0.6697 (ttm) cc_final: 0.6489 (ttm) REVERT: D 182 GLU cc_start: 0.8773 (mp0) cc_final: 0.8396 (mp0) REVERT: C 57 LYS cc_start: 0.9598 (ttmm) cc_final: 0.9248 (pttp) REVERT: C 178 TYR cc_start: 0.9199 (m-80) cc_final: 0.8823 (m-80) REVERT: C 182 GLU cc_start: 0.8803 (mp0) cc_final: 0.8331 (mp0) REVERT: C 324 MET cc_start: 0.9087 (tpp) cc_final: 0.8885 (tpp) REVERT: B 170 MET cc_start: 0.6587 (ttm) cc_final: 0.6336 (ttm) REVERT: B 182 GLU cc_start: 0.8838 (mp0) cc_final: 0.8462 (mp0) outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 0.6525 time to fit residues: 70.5490 Evaluate side-chains 95 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain B residue 64 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.101627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.072427 restraints weight = 18298.883| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.85 r_work: 0.3003 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8590 Z= 0.144 Angle : 0.571 7.446 11730 Z= 0.281 Chirality : 0.037 0.131 1490 Planarity : 0.004 0.031 1385 Dihedral : 4.275 20.330 1155 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.94 % Allowed : 20.34 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.26), residues: 1075 helix: 2.83 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.11 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 54 TYR 0.005 0.002 TYR E 178 PHE 0.008 0.001 PHE A 163 TRP 0.006 0.001 TRP A 344 HIS 0.010 0.005 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8590) covalent geometry : angle 0.57119 (11730) hydrogen bonds : bond 0.03483 ( 695) hydrogen bonds : angle 3.80282 ( 2055) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8674 (mp0) cc_final: 0.8242 (mp0) REVERT: E 182 GLU cc_start: 0.8674 (mp0) cc_final: 0.8249 (mp0) REVERT: D 182 GLU cc_start: 0.8760 (mp0) cc_final: 0.8331 (mp0) REVERT: D 294 VAL cc_start: 0.6996 (OUTLIER) cc_final: 0.6791 (t) REVERT: C 57 LYS cc_start: 0.9579 (ttmm) cc_final: 0.9282 (pttm) REVERT: C 178 TYR cc_start: 0.9240 (m-80) cc_final: 0.8700 (m-80) REVERT: C 182 GLU cc_start: 0.8767 (mp0) cc_final: 0.8263 (mp0) REVERT: B 182 GLU cc_start: 0.8835 (mp0) cc_final: 0.8438 (mp0) outliers start: 17 outliers final: 6 residues processed: 106 average time/residue: 0.5732 time to fit residues: 64.6645 Evaluate side-chains 94 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 99 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.102166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.073052 restraints weight = 18785.567| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.88 r_work: 0.3016 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8590 Z= 0.120 Angle : 0.553 7.896 11730 Z= 0.273 Chirality : 0.036 0.136 1490 Planarity : 0.004 0.033 1385 Dihedral : 4.217 20.054 1155 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.60 % Allowed : 24.11 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.26), residues: 1075 helix: 2.95 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.00 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 194 TYR 0.005 0.001 TYR E 178 PHE 0.006 0.001 PHE B 163 TRP 0.006 0.001 TRP B 277 HIS 0.009 0.004 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8590) covalent geometry : angle 0.55270 (11730) hydrogen bonds : bond 0.03241 ( 695) hydrogen bonds : angle 3.69323 ( 2055) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8677 (mp0) cc_final: 0.8282 (mp0) REVERT: E 57 LYS cc_start: 0.9664 (ttmm) cc_final: 0.9323 (ptmm) REVERT: E 182 GLU cc_start: 0.8665 (mp0) cc_final: 0.8218 (mp0) REVERT: D 182 GLU cc_start: 0.8747 (mp0) cc_final: 0.8297 (mp0) REVERT: D 294 VAL cc_start: 0.6795 (OUTLIER) cc_final: 0.6575 (t) REVERT: C 178 TYR cc_start: 0.9095 (m-80) cc_final: 0.8544 (m-80) REVERT: C 182 GLU cc_start: 0.8760 (mp0) cc_final: 0.8218 (mp0) REVERT: B 182 GLU cc_start: 0.8814 (mp0) cc_final: 0.8393 (mp0) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.5883 time to fit residues: 65.0715 Evaluate side-chains 99 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.0770 chunk 58 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.0060 overall best weight: 0.9358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072879 restraints weight = 18498.035| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.87 r_work: 0.3009 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8590 Z= 0.125 Angle : 0.542 8.121 11730 Z= 0.267 Chirality : 0.036 0.133 1490 Planarity : 0.004 0.033 1385 Dihedral : 4.146 19.678 1155 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.60 % Allowed : 26.63 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.26), residues: 1075 helix: 3.00 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.96 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 194 TYR 0.004 0.001 TYR B 178 PHE 0.007 0.001 PHE A 163 TRP 0.005 0.001 TRP A 344 HIS 0.008 0.004 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8590) covalent geometry : angle 0.54158 (11730) hydrogen bonds : bond 0.03136 ( 695) hydrogen bonds : angle 3.62483 ( 2055) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8698 (mp0) cc_final: 0.8287 (mp0) REVERT: E 57 LYS cc_start: 0.9655 (ttmm) cc_final: 0.9321 (ptmm) REVERT: E 182 GLU cc_start: 0.8664 (mp0) cc_final: 0.8208 (mp0) REVERT: D 182 GLU cc_start: 0.8782 (mp0) cc_final: 0.8295 (mp0) REVERT: D 294 VAL cc_start: 0.6770 (OUTLIER) cc_final: 0.6568 (t) REVERT: C 182 GLU cc_start: 0.8783 (mp0) cc_final: 0.8240 (mp0) REVERT: B 182 GLU cc_start: 0.8818 (mp0) cc_final: 0.8374 (mp0) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.6128 time to fit residues: 67.6896 Evaluate side-chains 101 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 21 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.101812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072737 restraints weight = 18582.245| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.87 r_work: 0.3007 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8590 Z= 0.128 Angle : 0.546 9.795 11730 Z= 0.268 Chirality : 0.036 0.132 1490 Planarity : 0.004 0.033 1385 Dihedral : 4.125 19.597 1155 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.06 % Allowed : 28.34 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.33 (0.26), residues: 1075 helix: 3.04 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.97 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 54 TYR 0.012 0.002 TYR C 178 PHE 0.006 0.001 PHE B 163 TRP 0.005 0.001 TRP A 344 HIS 0.007 0.004 HIS D 166 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8590) covalent geometry : angle 0.54561 (11730) hydrogen bonds : bond 0.03099 ( 695) hydrogen bonds : angle 3.59746 ( 2055) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8723 (mp0) cc_final: 0.8301 (mp0) REVERT: E 182 GLU cc_start: 0.8671 (mp0) cc_final: 0.8206 (mp0) REVERT: E 284 TRP cc_start: 0.6419 (m100) cc_final: 0.6059 (m100) REVERT: D 182 GLU cc_start: 0.8776 (mp0) cc_final: 0.8282 (mp0) REVERT: C 57 LYS cc_start: 0.9602 (ttmm) cc_final: 0.9313 (pttm) REVERT: C 182 GLU cc_start: 0.8783 (mp0) cc_final: 0.8238 (mp0) REVERT: C 284 TRP cc_start: 0.6253 (m100) cc_final: 0.5805 (m100) REVERT: B 182 GLU cc_start: 0.8825 (mp0) cc_final: 0.8372 (mp0) outliers start: 18 outliers final: 10 residues processed: 106 average time/residue: 0.5749 time to fit residues: 64.8475 Evaluate side-chains 103 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.102340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.073294 restraints weight = 18526.283| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.87 r_work: 0.3019 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8590 Z= 0.112 Angle : 0.550 10.996 11730 Z= 0.268 Chirality : 0.036 0.143 1490 Planarity : 0.004 0.033 1385 Dihedral : 4.079 19.206 1155 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.74 % Allowed : 28.00 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.26), residues: 1075 helix: 3.11 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 194 TYR 0.011 0.002 TYR C 178 PHE 0.010 0.001 PHE A 34 TRP 0.005 0.001 TRP A 344 HIS 0.007 0.004 HIS D 166 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8590) covalent geometry : angle 0.54973 (11730) hydrogen bonds : bond 0.02998 ( 695) hydrogen bonds : angle 3.54859 ( 2055) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8711 (mp0) cc_final: 0.8277 (mp0) REVERT: E 182 GLU cc_start: 0.8663 (mp0) cc_final: 0.8194 (mp0) REVERT: D 59 MET cc_start: 0.9001 (ttp) cc_final: 0.8736 (ttp) REVERT: D 182 GLU cc_start: 0.8764 (mp0) cc_final: 0.8284 (mp0) REVERT: D 313 SER cc_start: 0.9165 (t) cc_final: 0.8738 (m) REVERT: C 57 LYS cc_start: 0.9620 (ttmm) cc_final: 0.9404 (pttm) REVERT: C 59 MET cc_start: 0.9016 (mtm) cc_final: 0.8770 (ttp) REVERT: C 182 GLU cc_start: 0.8770 (mp0) cc_final: 0.8220 (mp0) REVERT: C 284 TRP cc_start: 0.6285 (m100) cc_final: 0.5874 (m100) REVERT: B 182 GLU cc_start: 0.8808 (mp0) cc_final: 0.8352 (mp0) outliers start: 24 outliers final: 10 residues processed: 115 average time/residue: 0.5300 time to fit residues: 65.0665 Evaluate side-chains 104 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 60 optimal weight: 0.0040 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.101931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.073071 restraints weight = 18429.311| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.87 r_work: 0.3012 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8590 Z= 0.123 Angle : 0.564 11.811 11730 Z= 0.273 Chirality : 0.036 0.130 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.034 19.336 1155 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.17 % Allowed : 29.26 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.26), residues: 1075 helix: 3.10 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.93 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 194 TYR 0.005 0.001 TYR E 178 PHE 0.014 0.001 PHE D 34 TRP 0.005 0.001 TRP A 344 HIS 0.007 0.004 HIS D 166 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8590) covalent geometry : angle 0.56415 (11730) hydrogen bonds : bond 0.02999 ( 695) hydrogen bonds : angle 3.55841 ( 2055) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8741 (mp0) cc_final: 0.8308 (mp0) REVERT: E 71 THR cc_start: 0.8798 (m) cc_final: 0.8590 (m) REVERT: E 182 GLU cc_start: 0.8677 (mp0) cc_final: 0.8203 (mp0) REVERT: D 59 MET cc_start: 0.8949 (ttp) cc_final: 0.8680 (ttp) REVERT: D 182 GLU cc_start: 0.8804 (mp0) cc_final: 0.8293 (mp0) REVERT: D 313 SER cc_start: 0.9213 (t) cc_final: 0.8749 (m) REVERT: C 59 MET cc_start: 0.9006 (mtm) cc_final: 0.8757 (ttp) REVERT: C 182 GLU cc_start: 0.8772 (mp0) cc_final: 0.8204 (mp0) REVERT: C 284 TRP cc_start: 0.6244 (m100) cc_final: 0.5828 (m100) REVERT: B 182 GLU cc_start: 0.8835 (mp0) cc_final: 0.8363 (mp0) outliers start: 19 outliers final: 10 residues processed: 114 average time/residue: 0.5076 time to fit residues: 61.7766 Evaluate side-chains 102 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.100596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071334 restraints weight = 18545.258| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.88 r_work: 0.2978 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8590 Z= 0.189 Angle : 0.620 12.393 11730 Z= 0.299 Chirality : 0.037 0.126 1490 Planarity : 0.004 0.031 1385 Dihedral : 4.119 19.807 1155 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.74 % Allowed : 28.69 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.26), residues: 1075 helix: 2.99 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.05 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 301 TYR 0.007 0.001 TYR B 178 PHE 0.013 0.001 PHE D 34 TRP 0.006 0.001 TRP B 277 HIS 0.007 0.005 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8590) covalent geometry : angle 0.62030 (11730) hydrogen bonds : bond 0.03246 ( 695) hydrogen bonds : angle 3.68220 ( 2055) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8774 (mp0) cc_final: 0.8299 (mp0) REVERT: A 284 TRP cc_start: 0.6391 (m100) cc_final: 0.6067 (m100) REVERT: E 71 THR cc_start: 0.8824 (m) cc_final: 0.8613 (m) REVERT: E 182 GLU cc_start: 0.8709 (mp0) cc_final: 0.8233 (mp0) REVERT: D 59 MET cc_start: 0.8954 (ttp) cc_final: 0.8664 (ttp) REVERT: D 182 GLU cc_start: 0.8812 (mp0) cc_final: 0.8296 (mp0) REVERT: D 313 SER cc_start: 0.9192 (t) cc_final: 0.8742 (m) REVERT: C 182 GLU cc_start: 0.8785 (mp0) cc_final: 0.8223 (mp0) REVERT: C 284 TRP cc_start: 0.6190 (m100) cc_final: 0.5790 (m100) REVERT: B 182 GLU cc_start: 0.8813 (mp0) cc_final: 0.8350 (mp0) REVERT: B 284 TRP cc_start: 0.6401 (m100) cc_final: 0.6124 (m100) outliers start: 24 outliers final: 13 residues processed: 116 average time/residue: 0.5675 time to fit residues: 70.1053 Evaluate side-chains 105 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.101753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072981 restraints weight = 18503.820| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.82 r_work: 0.3009 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8590 Z= 0.130 Angle : 0.648 13.590 11730 Z= 0.306 Chirality : 0.036 0.182 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.095 19.314 1155 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.49 % Allowed : 29.94 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.26), residues: 1075 helix: 2.95 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.98 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.006 0.001 TYR E 178 PHE 0.012 0.001 PHE D 34 TRP 0.005 0.001 TRP D 344 HIS 0.007 0.004 HIS D 166 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8590) covalent geometry : angle 0.64799 (11730) hydrogen bonds : bond 0.03175 ( 695) hydrogen bonds : angle 3.65374 ( 2055) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.9669 (ttmm) cc_final: 0.9434 (tmmt) REVERT: A 164 MET cc_start: 0.7244 (tmm) cc_final: 0.7027 (tpp) REVERT: A 182 GLU cc_start: 0.8749 (mp0) cc_final: 0.8273 (mp0) REVERT: A 313 SER cc_start: 0.9114 (t) cc_final: 0.8755 (m) REVERT: E 182 GLU cc_start: 0.8722 (mp0) cc_final: 0.8260 (mp0) REVERT: E 284 TRP cc_start: 0.6336 (m100) cc_final: 0.5953 (m100) REVERT: D 59 MET cc_start: 0.8963 (ttp) cc_final: 0.8692 (ttp) REVERT: D 182 GLU cc_start: 0.8802 (mp0) cc_final: 0.8292 (mp0) REVERT: D 313 SER cc_start: 0.9195 (t) cc_final: 0.8746 (m) REVERT: C 182 GLU cc_start: 0.8764 (mp0) cc_final: 0.8203 (mp0) REVERT: C 284 TRP cc_start: 0.6242 (m100) cc_final: 0.5848 (m100) REVERT: B 182 GLU cc_start: 0.8803 (mp0) cc_final: 0.8349 (mp0) REVERT: B 284 TRP cc_start: 0.6317 (m100) cc_final: 0.5935 (m100) outliers start: 13 outliers final: 8 residues processed: 105 average time/residue: 0.6075 time to fit residues: 67.7520 Evaluate side-chains 100 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 0.0670 chunk 24 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.102666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073634 restraints weight = 18343.969| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.85 r_work: 0.3026 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8590 Z= 0.120 Angle : 0.644 13.301 11730 Z= 0.305 Chirality : 0.036 0.182 1490 Planarity : 0.004 0.033 1385 Dihedral : 4.022 18.718 1155 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.03 % Allowed : 30.74 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.26), residues: 1075 helix: 3.01 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 301 TYR 0.006 0.001 TYR B 178 PHE 0.012 0.001 PHE D 34 TRP 0.007 0.001 TRP B 284 HIS 0.007 0.004 HIS D 166 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8590) covalent geometry : angle 0.64366 (11730) hydrogen bonds : bond 0.03046 ( 695) hydrogen bonds : angle 3.59453 ( 2055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2553.86 seconds wall clock time: 44 minutes 6.99 seconds (2646.99 seconds total)