Starting phenix.real_space_refine on Sat May 2 06:54:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t5k_55586/05_2026/9t5k_55586.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t5k_55586/05_2026/9t5k_55586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t5k_55586/05_2026/9t5k_55586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t5k_55586/05_2026/9t5k_55586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t5k_55586/05_2026/9t5k_55586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t5k_55586/05_2026/9t5k_55586.map" } resolution = 2.6 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= 0.001 sd= 0.017 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 15 5.16 5 C 1936 2.51 5 N 515 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3030 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3030 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 3 Time building chain proxies: 0.85, per 1000 atoms: 0.28 Number of scatterers: 3030 At special positions: 0 Unit cell: (69, 85.56, 86.48, 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 15 16.00 O 564 8.00 N 515 7.00 C 1936 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: 0.19 Conformation dependent library (CDL) restraints added in 98.1 milliseconds 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 71.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 Processing helix chain 'A' and resid 45 through 61 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 124 through 136 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.882A pdb=" N ASP A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 149' Processing helix chain 'A' and resid 154 through 177 removed outlier: 3.579A pdb=" N LEU A 172 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.575A pdb=" N LEU A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 221 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.626A pdb=" N LYS A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 259 Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.719A pdb=" N VAL A 280 " --> pdb=" O PRO A 277 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASN A 282 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU A 283 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 299 removed outlier: 3.572A pdb=" N ARG A 296 " --> pdb=" O GLN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 306 Proline residue: A 303 - end of helix Proline residue: A 306 - end of helix No H-bonds generated for 'chain 'A' and resid 300 through 306' Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 323 Proline residue: A 321 - end of helix Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.505A pdb=" N THR A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 384 through 397 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 180 hydrogen bonds defined for protein. 513 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: 0.32 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 988 1.34 - 1.46: 578 1.46 - 1.57: 1489 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3085 Sorted by residual: bond pdb=" CB GLU A 151 " pdb=" CG GLU A 151 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.85e-01 bond pdb=" CG GLU A 151 " pdb=" CD GLU A 151 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.17e-01 bond pdb=" CB VAL A 206 " pdb=" CG2 VAL A 206 " ideal model delta sigma weight residual 1.521 1.503 0.018 3.30e-02 9.18e+02 3.05e-01 bond pdb=" CB GLN A 125 " pdb=" CG GLN A 125 " ideal model delta sigma weight residual 1.520 1.534 -0.014 3.00e-02 1.11e+03 2.30e-01 bond pdb=" CB GLN A 138 " pdb=" CG GLN A 138 " ideal model delta sigma weight residual 1.520 1.534 -0.014 3.00e-02 1.11e+03 2.25e-01 ... (remaining 3080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 4064 0.98 - 1.96: 76 1.96 - 2.94: 25 2.94 - 3.92: 6 3.92 - 4.90: 3 Bond angle restraints: 4174 Sorted by residual: angle pdb=" CB GLU A 151 " pdb=" CG GLU A 151 " pdb=" CD GLU A 151 " ideal model delta sigma weight residual 112.60 116.35 -3.75 1.70e+00 3.46e-01 4.87e+00 angle pdb=" CA GLU A 151 " pdb=" CB GLU A 151 " pdb=" CG GLU A 151 " ideal model delta sigma weight residual 114.10 118.18 -4.08 2.00e+00 2.50e-01 4.17e+00 angle pdb=" N GLN A 383 " pdb=" CA GLN A 383 " pdb=" CB GLN A 383 " ideal model delta sigma weight residual 113.65 110.96 2.69 1.47e+00 4.63e-01 3.34e+00 angle pdb=" CB MET A 332 " pdb=" CG MET A 332 " pdb=" SD MET A 332 " ideal model delta sigma weight residual 112.70 117.60 -4.90 3.00e+00 1.11e-01 2.67e+00 angle pdb=" CA GLN A 383 " pdb=" C GLN A 383 " pdb=" N GLU A 384 " ideal model delta sigma weight residual 118.87 117.06 1.81 1.18e+00 7.18e-01 2.35e+00 ... (remaining 4169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.07: 1575 14.07 - 28.13: 205 28.13 - 42.19: 61 42.19 - 56.26: 29 56.26 - 70.32: 10 Dihedral angle restraints: 1880 sinusoidal: 767 harmonic: 1113 Sorted by residual: dihedral pdb=" CA ARG A 135 " pdb=" CB ARG A 135 " pdb=" CG ARG A 135 " pdb=" CD ARG A 135 " ideal model delta sinusoidal sigma weight residual -60.00 -119.05 59.05 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLN A 196 " pdb=" CB GLN A 196 " pdb=" CG GLN A 196 " pdb=" CD GLN A 196 " ideal model delta sinusoidal sigma weight residual 180.00 -121.43 -58.57 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N GLN A 385 " pdb=" CA GLN A 385 " pdb=" CB GLN A 385 " pdb=" CG GLN A 385 " ideal model delta sinusoidal sigma weight residual -180.00 -122.42 -57.58 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 286 0.025 - 0.051: 109 0.051 - 0.076: 57 0.076 - 0.101: 16 0.101 - 0.126: 9 Chirality restraints: 477 Sorted by residual: chirality pdb=" CA ILE A 36 " pdb=" N ILE A 36 " pdb=" C ILE A 36 " pdb=" CB ILE A 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL A 101 " pdb=" N VAL A 101 " pdb=" C VAL A 101 " pdb=" CB VAL A 101 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA VAL A 112 " pdb=" N VAL A 112 " pdb=" C VAL A 112 " pdb=" CB VAL A 112 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 474 not shown) Planarity restraints: 531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 305 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 306 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 276 " -0.013 5.00e-02 4.00e+02 1.98e-02 6.25e-01 pdb=" N PRO A 277 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 320 " -0.013 5.00e-02 4.00e+02 1.97e-02 6.22e-01 pdb=" N PRO A 321 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.011 5.00e-02 4.00e+02 ... (remaining 528 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 167 2.74 - 3.28: 3041 3.28 - 3.82: 5015 3.82 - 4.36: 5920 4.36 - 4.90: 10080 Nonbonded interactions: 24223 Sorted by model distance: nonbonded pdb=" N GLU A 151 " pdb=" OE1 GLU A 151 " model vdw 2.195 3.120 nonbonded pdb=" O THR A 398 " pdb=" OG1 THR A 398 " model vdw 2.286 3.040 nonbonded pdb=" OG SER A 62 " pdb=" O ILE A 132 " model vdw 2.325 3.040 nonbonded pdb=" OG SER A 79 " pdb=" OH TYR A 227 " model vdw 2.333 3.040 nonbonded pdb=" NH2 ARG A 49 " pdb=" O GLU A 83 " model vdw 2.343 3.120 ... (remaining 24218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 5.540 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.530 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.002 0.030 3085 Z= 0.087 Angle : 0.403 4.898 4174 Z= 0.215 Chirality : 0.037 0.126 477 Planarity : 0.003 0.026 531 Dihedral : 15.741 70.324 1158 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.61 % Allowed : 19.82 % Favored : 79.57 % 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: 0.82 (0.43), residues: 373 helix: 0.71 (0.34), residues: 251 sheet: None (None), residues: 0 loop : 0.49 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 49 TYR 0.013 0.001 TYR A 356 PHE 0.009 0.001 PHE A 158 TRP 0.011 0.001 TRP A 210 HIS 0.001 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 3085) covalent geometry : angle 0.40251 ( 4174) hydrogen bonds : bond 0.18386 ( 180) hydrogen bonds : angle 5.76964 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.120 Fit side-chains REVERT: A 14 GLU cc_start: 0.8211 (tt0) cc_final: 0.7457 (tp30) REVERT: A 44 LYS cc_start: 0.8870 (mtmt) cc_final: 0.7859 (tptp) REVERT: A 114 ARG cc_start: 0.7505 (ttt180) cc_final: 0.7078 (ttp-110) REVERT: A 188 ASN cc_start: 0.6820 (m-40) cc_final: 0.6489 (p0) REVERT: A 189 LYS cc_start: 0.8766 (tttp) cc_final: 0.7925 (mptt) REVERT: A 365 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7073 (tpm170) REVERT: A 373 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.6513 (mtm180) REVERT: A 392 MET cc_start: 0.8178 (ttm) cc_final: 0.7959 (ttp) outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 0.7247 time to fit residues: 36.2258 Evaluate side-chains 46 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.116201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098085 restraints weight = 3936.506| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.16 r_work: 0.3010 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3085 Z= 0.119 Angle : 0.451 4.181 4174 Z= 0.236 Chirality : 0.040 0.127 477 Planarity : 0.003 0.028 531 Dihedral : 3.566 15.895 415 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.96 % Allowed : 15.55 % Favored : 80.49 % 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: 1.83 (0.45), residues: 373 helix: 1.47 (0.34), residues: 248 sheet: None (None), residues: 0 loop : 0.94 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.014 0.001 TYR A 356 PHE 0.012 0.001 PHE A 158 TRP 0.012 0.001 TRP A 210 HIS 0.001 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3085) covalent geometry : angle 0.45069 ( 4174) hydrogen bonds : bond 0.03543 ( 180) hydrogen bonds : angle 3.76755 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.126 Fit side-chains REVERT: A 14 GLU cc_start: 0.8058 (tt0) cc_final: 0.7351 (tp30) REVERT: A 44 LYS cc_start: 0.8925 (mtmt) cc_final: 0.7845 (tptp) REVERT: A 114 ARG cc_start: 0.7440 (ttt180) cc_final: 0.7029 (ttp-110) REVERT: A 189 LYS cc_start: 0.8310 (tttp) cc_final: 0.7539 (pmtt) REVERT: A 365 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7023 (tpm170) REVERT: A 373 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.6301 (mtm180) REVERT: A 374 LYS cc_start: 0.8611 (ttmt) cc_final: 0.7952 (mptt) REVERT: A 385 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6852 (mt0) outliers start: 13 outliers final: 6 residues processed: 56 average time/residue: 0.7234 time to fit residues: 41.2790 Evaluate side-chains 54 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 385 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.096664 restraints weight = 3988.042| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.18 r_work: 0.3007 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3085 Z= 0.144 Angle : 0.451 4.235 4174 Z= 0.236 Chirality : 0.040 0.125 477 Planarity : 0.003 0.028 531 Dihedral : 3.519 16.493 413 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.35 % Allowed : 16.46 % Favored : 80.18 % 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: 1.95 (0.44), residues: 373 helix: 1.64 (0.34), residues: 247 sheet: None (None), residues: 0 loop : 0.81 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 49 TYR 0.015 0.001 TYR A 356 PHE 0.013 0.001 PHE A 158 TRP 0.012 0.001 TRP A 210 HIS 0.001 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3085) covalent geometry : angle 0.45066 ( 4174) hydrogen bonds : bond 0.03487 ( 180) hydrogen bonds : angle 3.69654 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.079 Fit side-chains REVERT: A 14 GLU cc_start: 0.8107 (tt0) cc_final: 0.7406 (tp30) REVERT: A 44 LYS cc_start: 0.8901 (mtmt) cc_final: 0.7814 (tptp) REVERT: A 114 ARG cc_start: 0.7469 (ttt180) cc_final: 0.7056 (ttp-110) REVERT: A 189 LYS cc_start: 0.8345 (tttp) cc_final: 0.7554 (pmtt) REVERT: A 340 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7454 (ptp-170) REVERT: A 365 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7048 (tpm170) REVERT: A 373 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.6202 (mtm180) REVERT: A 374 LYS cc_start: 0.8621 (ttmt) cc_final: 0.7940 (mptt) REVERT: A 383 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7519 (tp-100) REVERT: A 385 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.7000 (mt0) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 0.7172 time to fit residues: 39.4582 Evaluate side-chains 54 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 385 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 0.0570 chunk 1 optimal weight: 0.0470 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.0470 chunk 37 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 22 GLN ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100848 restraints weight = 3961.330| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.15 r_work: 0.3062 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3085 Z= 0.078 Angle : 0.395 4.198 4174 Z= 0.208 Chirality : 0.038 0.127 477 Planarity : 0.003 0.027 531 Dihedral : 3.336 15.547 413 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.66 % Allowed : 17.99 % Favored : 78.35 % 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: 2.32 (0.44), residues: 373 helix: 1.95 (0.34), residues: 248 sheet: None (None), residues: 0 loop : 0.88 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.011 0.001 TYR A 356 PHE 0.010 0.001 PHE A 158 TRP 0.010 0.001 TRP A 210 HIS 0.000 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00162 ( 3085) covalent geometry : angle 0.39521 ( 4174) hydrogen bonds : bond 0.02730 ( 180) hydrogen bonds : angle 3.46558 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.074 Fit side-chains REVERT: A 14 GLU cc_start: 0.8033 (tt0) cc_final: 0.7400 (tp30) REVERT: A 44 LYS cc_start: 0.8941 (mtmt) cc_final: 0.7831 (tptp) REVERT: A 114 ARG cc_start: 0.7483 (ttt180) cc_final: 0.7098 (ttp-110) REVERT: A 189 LYS cc_start: 0.8318 (tttp) cc_final: 0.7528 (pmtt) REVERT: A 339 ASP cc_start: 0.7996 (t0) cc_final: 0.7725 (t0) REVERT: A 365 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7035 (tpm170) REVERT: A 373 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.5936 (mtp180) REVERT: A 374 LYS cc_start: 0.8633 (ttmt) cc_final: 0.7950 (mptt) outliers start: 12 outliers final: 4 residues processed: 57 average time/residue: 0.6669 time to fit residues: 38.8335 Evaluate side-chains 51 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 391 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 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 16 GLN A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097021 restraints weight = 4024.631| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.11 r_work: 0.3019 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3085 Z= 0.168 Angle : 0.466 4.607 4174 Z= 0.243 Chirality : 0.041 0.125 477 Planarity : 0.003 0.028 531 Dihedral : 3.554 17.458 413 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.96 % Allowed : 17.07 % Favored : 78.96 % 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: 2.03 (0.44), residues: 373 helix: 1.87 (0.34), residues: 247 sheet: -1.95 (1.03), residues: 10 loop : 0.69 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 209 TYR 0.017 0.001 TYR A 356 PHE 0.014 0.001 PHE A 158 TRP 0.013 0.001 TRP A 210 HIS 0.001 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 3085) covalent geometry : angle 0.46619 ( 4174) hydrogen bonds : bond 0.03409 ( 180) hydrogen bonds : angle 3.63254 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.167 Fit side-chains REVERT: A 14 GLU cc_start: 0.8125 (tt0) cc_final: 0.7464 (tp30) REVERT: A 44 LYS cc_start: 0.8907 (mtmt) cc_final: 0.7811 (tptp) REVERT: A 114 ARG cc_start: 0.7451 (ttt180) cc_final: 0.7055 (ttp-110) REVERT: A 189 LYS cc_start: 0.8409 (tttp) cc_final: 0.7588 (pmtt) REVERT: A 340 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7536 (ptp-170) REVERT: A 365 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7014 (tpm170) REVERT: A 373 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.5937 (mtp180) REVERT: A 374 LYS cc_start: 0.8643 (ttmt) cc_final: 0.7938 (mptt) REVERT: A 383 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7498 (tp-100) REVERT: A 385 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6931 (mt0) outliers start: 13 outliers final: 4 residues processed: 55 average time/residue: 0.7376 time to fit residues: 41.3548 Evaluate side-chains 51 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 385 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 25 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: A 22 GLN ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097491 restraints weight = 4027.901| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.11 r_work: 0.3028 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3085 Z= 0.146 Angle : 0.456 4.192 4174 Z= 0.238 Chirality : 0.040 0.125 477 Planarity : 0.003 0.029 531 Dihedral : 3.576 18.606 413 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.27 % Allowed : 16.77 % Favored : 78.96 % 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: 2.13 (0.44), residues: 373 helix: 1.82 (0.34), residues: 248 sheet: None (None), residues: 0 loop : 0.75 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 215 TYR 0.016 0.001 TYR A 356 PHE 0.014 0.001 PHE A 158 TRP 0.012 0.001 TRP A 210 HIS 0.001 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3085) covalent geometry : angle 0.45622 ( 4174) hydrogen bonds : bond 0.03246 ( 180) hydrogen bonds : angle 3.60389 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.103 Fit side-chains REVERT: A 14 GLU cc_start: 0.8089 (tt0) cc_final: 0.7458 (tp30) REVERT: A 44 LYS cc_start: 0.8878 (mtmt) cc_final: 0.7792 (tptp) REVERT: A 114 ARG cc_start: 0.7469 (ttt180) cc_final: 0.7085 (ttp-110) REVERT: A 189 LYS cc_start: 0.8424 (tttp) cc_final: 0.7596 (pmtt) REVERT: A 340 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7488 (ptp-170) REVERT: A 365 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7056 (tpm170) REVERT: A 373 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.5919 (mtp180) REVERT: A 374 LYS cc_start: 0.8694 (ttmt) cc_final: 0.7997 (mptt) REVERT: A 383 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7553 (tp-100) REVERT: A 385 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6967 (mt0) outliers start: 14 outliers final: 6 residues processed: 54 average time/residue: 0.7245 time to fit residues: 39.8462 Evaluate side-chains 52 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 385 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096968 restraints weight = 4081.134| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.13 r_work: 0.3017 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3085 Z= 0.153 Angle : 0.463 4.195 4174 Z= 0.240 Chirality : 0.040 0.125 477 Planarity : 0.003 0.029 531 Dihedral : 3.589 18.020 413 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.35 % Allowed : 17.99 % Favored : 78.66 % 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: 2.11 (0.44), residues: 373 helix: 1.82 (0.34), residues: 248 sheet: None (None), residues: 0 loop : 0.72 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 215 TYR 0.016 0.001 TYR A 356 PHE 0.014 0.001 PHE A 158 TRP 0.012 0.001 TRP A 210 HIS 0.001 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 3085) covalent geometry : angle 0.46319 ( 4174) hydrogen bonds : bond 0.03278 ( 180) hydrogen bonds : angle 3.62827 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.076 Fit side-chains REVERT: A 14 GLU cc_start: 0.8093 (tt0) cc_final: 0.7454 (tp30) REVERT: A 44 LYS cc_start: 0.8855 (mtmt) cc_final: 0.7712 (tptt) REVERT: A 114 ARG cc_start: 0.7487 (ttt180) cc_final: 0.7098 (ttp-110) REVERT: A 124 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 189 LYS cc_start: 0.8394 (tttp) cc_final: 0.7584 (pmtt) REVERT: A 340 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7443 (ptp-170) REVERT: A 342 MET cc_start: 0.7395 (ttt) cc_final: 0.7121 (ttt) REVERT: A 365 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7042 (tpm170) REVERT: A 373 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.5923 (mtp180) REVERT: A 374 LYS cc_start: 0.8691 (ttmt) cc_final: 0.7994 (mptt) REVERT: A 383 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7529 (tp-100) REVERT: A 385 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7033 (mt0) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 0.7195 time to fit residues: 38.1217 Evaluate side-chains 53 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 385 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.0070 chunk 9 optimal weight: 0.8980 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 22 GLN ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099121 restraints weight = 4072.095| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.21 r_work: 0.3035 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3085 Z= 0.095 Angle : 0.419 4.757 4174 Z= 0.219 Chirality : 0.038 0.127 477 Planarity : 0.003 0.029 531 Dihedral : 3.429 17.167 413 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.13 % Allowed : 19.82 % Favored : 78.05 % 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: 2.36 (0.44), residues: 373 helix: 2.03 (0.34), residues: 248 sheet: None (None), residues: 0 loop : 0.77 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 225 TYR 0.013 0.001 TYR A 356 PHE 0.011 0.001 PHE A 158 TRP 0.010 0.001 TRP A 210 HIS 0.001 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 3085) covalent geometry : angle 0.41897 ( 4174) hydrogen bonds : bond 0.02777 ( 180) hydrogen bonds : angle 3.46736 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.168 Fit side-chains REVERT: A 14 GLU cc_start: 0.8104 (tt0) cc_final: 0.7476 (tp30) REVERT: A 44 LYS cc_start: 0.8863 (mtmt) cc_final: 0.7716 (tptt) REVERT: A 114 ARG cc_start: 0.7479 (ttt180) cc_final: 0.7054 (ttp-110) REVERT: A 124 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 189 LYS cc_start: 0.8302 (tttp) cc_final: 0.7519 (pmtt) REVERT: A 339 ASP cc_start: 0.7955 (t0) cc_final: 0.7691 (t0) REVERT: A 342 MET cc_start: 0.7446 (ttt) cc_final: 0.6924 (ttt) REVERT: A 365 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7027 (tpm170) REVERT: A 373 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.5871 (mtp180) REVERT: A 383 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7340 (tp-100) REVERT: A 385 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6940 (mt0) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.7582 time to fit residues: 40.1988 Evaluate side-chains 52 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 391 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097536 restraints weight = 4117.772| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.13 r_work: 0.3029 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3085 Z= 0.141 Angle : 0.447 4.271 4174 Z= 0.231 Chirality : 0.040 0.123 477 Planarity : 0.003 0.027 531 Dihedral : 3.523 17.616 413 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.35 % Allowed : 18.29 % Favored : 78.35 % 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: 2.25 (0.44), residues: 373 helix: 1.95 (0.34), residues: 248 sheet: None (None), residues: 0 loop : 0.70 (0.55), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 209 TYR 0.015 0.001 TYR A 356 PHE 0.014 0.001 PHE A 158 TRP 0.012 0.001 TRP A 210 HIS 0.001 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3085) covalent geometry : angle 0.44742 ( 4174) hydrogen bonds : bond 0.03153 ( 180) hydrogen bonds : angle 3.56702 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.120 Fit side-chains REVERT: A 14 GLU cc_start: 0.8190 (tt0) cc_final: 0.7544 (tp30) REVERT: A 44 LYS cc_start: 0.8859 (mtmt) cc_final: 0.7740 (tptp) REVERT: A 114 ARG cc_start: 0.7477 (ttt180) cc_final: 0.7092 (ttp-110) REVERT: A 124 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 151 GLU cc_start: 0.7872 (tp30) cc_final: 0.7638 (pm20) REVERT: A 189 LYS cc_start: 0.8400 (tttp) cc_final: 0.7591 (pmtt) REVERT: A 342 MET cc_start: 0.7426 (ttt) cc_final: 0.7133 (ttt) REVERT: A 365 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7031 (tpm170) REVERT: A 373 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.6045 (mtp180) REVERT: A 383 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7498 (tp-100) REVERT: A 385 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6924 (mt0) outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 0.6814 time to fit residues: 38.9938 Evaluate side-chains 52 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 385 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 0.0050 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097577 restraints weight = 4015.685| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.11 r_work: 0.3031 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3085 Z= 0.137 Angle : 0.448 4.262 4174 Z= 0.232 Chirality : 0.040 0.125 477 Planarity : 0.003 0.028 531 Dihedral : 3.548 18.277 413 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.83 % Allowed : 19.82 % Favored : 78.35 % 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: 2.16 (0.44), residues: 373 helix: 1.85 (0.34), residues: 249 sheet: None (None), residues: 0 loop : 0.74 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 215 TYR 0.015 0.001 TYR A 356 PHE 0.013 0.001 PHE A 158 TRP 0.012 0.001 TRP A 210 HIS 0.001 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3085) covalent geometry : angle 0.44845 ( 4174) hydrogen bonds : bond 0.03128 ( 180) hydrogen bonds : angle 3.57709 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.124 Fit side-chains REVERT: A 14 GLU cc_start: 0.8178 (tt0) cc_final: 0.7539 (tp30) REVERT: A 44 LYS cc_start: 0.8868 (mtmt) cc_final: 0.7745 (tptp) REVERT: A 114 ARG cc_start: 0.7485 (ttt180) cc_final: 0.7100 (ttp-110) REVERT: A 124 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7446 (tm-30) REVERT: A 151 GLU cc_start: 0.7880 (tp30) cc_final: 0.7628 (pm20) REVERT: A 189 LYS cc_start: 0.8411 (tttp) cc_final: 0.7599 (pmtt) REVERT: A 342 MET cc_start: 0.7467 (ttt) cc_final: 0.7208 (ttt) REVERT: A 365 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7053 (tpm170) REVERT: A 373 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.6020 (mtp180) REVERT: A 383 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7535 (tp-100) REVERT: A 385 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7026 (mt0) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.6848 time to fit residues: 34.2609 Evaluate side-chains 51 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 395 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097766 restraints weight = 3997.473| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.15 r_work: 0.3025 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3085 Z= 0.115 Angle : 0.434 4.221 4174 Z= 0.224 Chirality : 0.039 0.126 477 Planarity : 0.003 0.028 531 Dihedral : 3.497 17.715 413 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.83 % Allowed : 19.82 % Favored : 78.35 % 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: 2.21 (0.44), residues: 373 helix: 1.90 (0.34), residues: 249 sheet: None (None), residues: 0 loop : 0.74 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 215 TYR 0.015 0.001 TYR A 356 PHE 0.012 0.001 PHE A 158 TRP 0.011 0.001 TRP A 210 HIS 0.001 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3085) covalent geometry : angle 0.43395 ( 4174) hydrogen bonds : bond 0.02992 ( 180) hydrogen bonds : angle 3.53278 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1457.37 seconds wall clock time: 25 minutes 33.16 seconds (1533.16 seconds total)