Starting phenix.real_space_refine on Tue Aug 4 18:14:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yyh_73645/08_2026/9yyh_73645.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yyh_73645/08_2026/9yyh_73645.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/9yyh_73645/08_2026/9yyh_73645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yyh_73645/08_2026/9yyh_73645.map" model { file = "/net/cci-nas-00/data/ceres_data/9yyh_73645/08_2026/9yyh_73645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yyh_73645/08_2026/9yyh_73645.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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 129 5.49 5 S 8 5.16 5 C 3189 2.51 5 N 1077 2.21 5 O 1406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5809 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3063 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2100 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 46, 'rna3p_pyr': 41} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain breaks: 2 Chain: "C" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "D" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 407 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 76 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Time building chain proxies: 1.57, per 1000 atoms: 0.27 Number of scatterers: 5809 At special positions: 0 Unit cell: (75.472, 104.304, 96.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 129 15.00 O 1406 8.00 N 1077 7.00 C 3189 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: 0.41 Conformation dependent library (CDL) restraints added in 284.6 milliseconds 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 710 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 50.9% alpha, 14.6% beta 43 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 14 through 46 removed outlier: 3.780A pdb=" N LEU A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.857A pdb=" N GLU A 73 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 75 through 100 removed outlier: 3.919A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.589A pdb=" N SER A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 272 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 359 through 377 removed outlier: 3.887A pdb=" N ALA A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 121 removed outlier: 3.800A pdb=" N LYS A 153 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 172 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A 157 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER A 170 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL A 159 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU A 168 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 145 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.622A pdb=" N ALA A 198 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A 191 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 188 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 275 " --> pdb=" O ALA A 319 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 109 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1198 1.33 - 1.45: 2023 1.45 - 1.57: 2708 1.57 - 1.69: 253 1.69 - 1.81: 12 Bond restraints: 6194 Sorted by residual: bond pdb=" C1' DA D 6 " pdb=" N9 DA D 6 " ideal model delta sigma weight residual 1.468 1.387 0.081 1.40e-02 5.10e+03 3.35e+01 bond pdb=" C1' DT C -6 " pdb=" N1 DT C -6 " ideal model delta sigma weight residual 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.47e+01 bond pdb=" C3' DT D 5 " pdb=" O3' DT D 5 " ideal model delta sigma weight residual 1.435 1.475 -0.040 1.30e-02 5.92e+03 9.63e+00 bond pdb=" C5 DC C -7 " pdb=" C6 DC C -7 " ideal model delta sigma weight residual 1.339 1.360 -0.021 8.00e-03 1.56e+04 6.96e+00 bond pdb=" C3' DG D -7 " pdb=" O3' DG D -7 " ideal model delta sigma weight residual 1.435 1.402 0.033 1.30e-02 5.92e+03 6.56e+00 ... (remaining 6189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 8353 1.55 - 3.10: 546 3.10 - 4.65: 44 4.65 - 6.20: 7 6.20 - 7.76: 6 Bond angle restraints: 8956 Sorted by residual: angle pdb=" C1' C B -92 " pdb=" N1 C B -92 " pdb=" C2 C B -92 " ideal model delta sigma weight residual 118.80 124.03 -5.23 1.10e+00 8.26e-01 2.26e+01 angle pdb=" C3' DT D 5 " pdb=" O3' DT D 5 " pdb=" P DA D 6 " ideal model delta sigma weight residual 119.70 125.21 -5.51 1.20e+00 6.94e-01 2.11e+01 angle pdb=" O5' C B-110 " pdb=" C5' C B-110 " pdb=" C4' C B-110 " ideal model delta sigma weight residual 109.40 112.88 -3.48 8.00e-01 1.56e+00 1.90e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C -3 " pdb=" C4 DT C -3 " pdb=" O4 DT C -3 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 ... (remaining 8951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 3126 23.79 - 47.59: 420 47.59 - 71.38: 218 71.38 - 95.18: 30 95.18 - 118.97: 1 Dihedral angle restraints: 3795 sinusoidal: 2701 harmonic: 1094 Sorted by residual: dihedral pdb=" O4' U B -89 " pdb=" C1' U B -89 " pdb=" N1 U B -89 " pdb=" C2 U B -89 " ideal model delta sinusoidal sigma weight residual -160.00 -84.99 -75.01 1 1.50e+01 4.44e-03 3.16e+01 dihedral pdb=" CA GLU A 204 " pdb=" C GLU A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta harmonic sigma weight residual -180.00 -159.77 -20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" O4' G B-115 " pdb=" C2' G B-115 " pdb=" C1' G B-115 " pdb=" C3' G B-115 " ideal model delta sinusoidal sigma weight residual 25.00 -1.95 26.95 1 8.00e+00 1.56e-02 1.63e+01 ... (remaining 3792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 754 0.046 - 0.092: 166 0.092 - 0.138: 125 0.138 - 0.184: 17 0.184 - 0.230: 5 Chirality restraints: 1067 Sorted by residual: chirality pdb=" C3' A B-103 " pdb=" C4' A B-103 " pdb=" O3' A B-103 " pdb=" C2' A B-103 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C3' DT D 5 " pdb=" C4' DT D 5 " pdb=" O3' DT D 5 " pdb=" C2' DT D 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C3' G B-104 " pdb=" C4' G B-104 " pdb=" O3' G B-104 " pdb=" C2' G B-104 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1064 not shown) Planarity restraints: 666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 338 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO A 339 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 106 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO A 107 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 351 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO A 352 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 352 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 352 " -0.033 5.00e-02 4.00e+02 ... (remaining 663 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1329 2.79 - 3.32: 5071 3.32 - 3.85: 11145 3.85 - 4.37: 12791 4.37 - 4.90: 18438 Nonbonded interactions: 48774 Sorted by model distance: nonbonded pdb=" NE2 GLN A 121 " pdb=" OP1 DA D 0 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR A 309 " pdb=" OP1 G B 1 " model vdw 2.282 3.040 nonbonded pdb=" NZ LYS A 220 " pdb=" OP1 A B -71 " model vdw 2.318 3.120 nonbonded pdb=" NZ LYS A 270 " pdb=" OP1 A B -1 " model vdw 2.328 3.120 nonbonded pdb=" OE1 GLN A 258 " pdb=" NE2 GLN A 306 " model vdw 2.330 3.120 ... (remaining 48769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 0.081 6194 Z= 0.383 Angle : 0.791 7.756 8956 Z= 0.622 Chirality : 0.058 0.230 1067 Planarity : 0.007 0.113 666 Dihedral : 22.919 118.970 3085 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.86 % Allowed : 18.27 % Favored : 79.88 % 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: 0.14 (0.43), residues: 375 helix: 1.56 (0.38), residues: 185 sheet: -1.62 (0.61), residues: 56 loop : -1.18 (0.50), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.014 0.002 TYR A 309 PHE 0.021 0.002 PHE A 118 TRP 0.012 0.002 TRP A 70 HIS 0.007 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.38 ( 6194) covalent geometry : angle 0.79143 / 0.62 ( 8956) hydrogen bonds : bond 0.14983 / 9.78 ( 272) hydrogen bonds : angle 5.46881 / 4.22 ( 655) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.155 Fit side-chains REVERT: A 370 ARG cc_start: 0.6731 (mtp180) cc_final: 0.6319 (mtp180) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 0.6497 time to fit residues: 41.2892 Evaluate side-chains 58 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 356 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.153337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135365 restraints weight = 8076.190| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.42 r_work: 0.3708 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6194 Z= 0.168 Angle : 0.574 11.456 8956 Z= 0.331 Chirality : 0.041 0.429 1067 Planarity : 0.006 0.075 666 Dihedral : 24.128 113.159 2300 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.02 % Allowed : 17.03 % Favored : 78.95 % 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: 0.34 (0.43), residues: 375 helix: 1.74 (0.38), residues: 187 sheet: -1.39 (0.65), residues: 56 loop : -1.22 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.029 0.002 TYR A 309 PHE 0.020 0.002 PHE A 118 TRP 0.010 0.001 TRP A 313 HIS 0.007 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 ( 6194) covalent geometry : angle 0.57448 / 0.33 ( 8956) hydrogen bonds : bond 0.07590 / 5.39 ( 272) hydrogen bonds : angle 3.74237 / 2.80 ( 655) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.149 Fit side-chains REVERT: A 83 LEU cc_start: 0.8414 (mm) cc_final: 0.8185 (mp) REVERT: A 304 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7953 (ttp80) REVERT: A 370 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6609 (mtp180) outliers start: 13 outliers final: 6 residues processed: 60 average time/residue: 0.6016 time to fit residues: 37.5534 Evaluate side-chains 62 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 348 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 18 optimal weight: 0.0970 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 GLN ** A 358 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 = 0.4025 r_free = 0.4025 target = 0.151690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.133734 restraints weight = 8028.924| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.40 r_work: 0.3690 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6194 Z= 0.209 Angle : 0.590 11.420 8956 Z= 0.336 Chirality : 0.043 0.426 1067 Planarity : 0.006 0.067 666 Dihedral : 24.017 111.605 2298 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.33 % Allowed : 17.65 % Favored : 78.02 % 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: 0.33 (0.43), residues: 375 helix: 1.69 (0.38), residues: 187 sheet: -1.25 (0.67), residues: 56 loop : -1.23 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 231 TYR 0.032 0.003 TYR A 309 PHE 0.027 0.003 PHE A 118 TRP 0.013 0.002 TRP A 313 HIS 0.008 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 ( 6194) covalent geometry : angle 0.59028 / 0.34 ( 8956) hydrogen bonds : bond 0.07759 / 5.46 ( 272) hydrogen bonds : angle 3.61456 / 2.70 ( 655) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.152 Fit side-chains REVERT: A 76 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7261 (pttp) REVERT: A 370 ARG cc_start: 0.7147 (mtp180) cc_final: 0.6648 (mtp180) outliers start: 14 outliers final: 8 residues processed: 62 average time/residue: 0.7131 time to fit residues: 45.9099 Evaluate side-chains 65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.153978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.136029 restraints weight = 8161.295| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.41 r_work: 0.3724 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6194 Z= 0.143 Angle : 0.520 11.558 8956 Z= 0.300 Chirality : 0.038 0.408 1067 Planarity : 0.005 0.061 666 Dihedral : 23.935 106.247 2298 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.41 % Allowed : 19.50 % Favored : 77.09 % 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: 0.43 (0.44), residues: 375 helix: 1.92 (0.38), residues: 187 sheet: -1.28 (0.58), residues: 72 loop : -1.36 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.027 0.002 TYR A 309 PHE 0.019 0.002 PHE A 118 TRP 0.006 0.001 TRP A 313 HIS 0.006 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 6194) covalent geometry : angle 0.51969 / 0.30 ( 8956) hydrogen bonds : bond 0.06737 / 4.81 ( 272) hydrogen bonds : angle 3.33521 / 2.48 ( 655) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.097 Fit side-chains REVERT: A 304 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7922 (ttp80) REVERT: A 370 ARG cc_start: 0.7139 (mtp180) cc_final: 0.6645 (mtp180) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.6880 time to fit residues: 40.6642 Evaluate side-chains 60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 348 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.0060 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.153631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135558 restraints weight = 8169.895| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.43 r_work: 0.3715 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6194 Z= 0.151 Angle : 0.516 11.498 8956 Z= 0.296 Chirality : 0.038 0.355 1067 Planarity : 0.005 0.061 666 Dihedral : 23.880 98.653 2294 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.02 % Allowed : 17.96 % Favored : 78.02 % 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: 0.56 (0.44), residues: 375 helix: 2.00 (0.38), residues: 186 sheet: -1.22 (0.58), residues: 72 loop : -1.22 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.026 0.002 TYR A 309 PHE 0.022 0.002 PHE A 118 TRP 0.006 0.001 TRP A 313 HIS 0.007 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 6194) covalent geometry : angle 0.51573 / 0.30 ( 8956) hydrogen bonds : bond 0.06643 / 4.74 ( 272) hydrogen bonds : angle 3.23908 / 2.41 ( 655) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.169 Fit side-chains REVERT: A 76 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7002 (pttp) REVERT: A 304 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7946 (ttp80) REVERT: A 370 ARG cc_start: 0.7156 (mtp180) cc_final: 0.6838 (mtp180) outliers start: 13 outliers final: 6 residues processed: 59 average time/residue: 0.6355 time to fit residues: 38.9303 Evaluate side-chains 60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 0.0870 chunk 42 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.151292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133212 restraints weight = 8123.269| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.41 r_work: 0.3683 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6194 Z= 0.227 Angle : 0.587 10.641 8956 Z= 0.330 Chirality : 0.042 0.218 1067 Planarity : 0.006 0.065 666 Dihedral : 23.856 89.603 2294 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.33 % Allowed : 17.34 % Favored : 78.33 % 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: 0.49 (0.43), residues: 375 helix: 1.81 (0.38), residues: 187 sheet: -1.10 (0.69), residues: 55 loop : -1.19 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.039 0.003 TYR A 309 PHE 0.031 0.003 PHE A 118 TRP 0.006 0.001 TRP A 300 HIS 0.008 0.002 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.23 ( 6194) covalent geometry : angle 0.58661 / 0.33 ( 8956) hydrogen bonds : bond 0.07612 / 5.33 ( 272) hydrogen bonds : angle 3.37065 / 2.50 ( 655) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.173 Fit side-chains REVERT: A 76 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7255 (pttp) REVERT: A 304 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7978 (ttp80) REVERT: A 343 ASP cc_start: 0.7485 (t0) cc_final: 0.7260 (t0) REVERT: A 370 ARG cc_start: 0.7140 (mtp180) cc_final: 0.6841 (mtp180) outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.5806 time to fit residues: 39.2898 Evaluate side-chains 66 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 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 = 0.4038 r_free = 0.4038 target = 0.152731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134555 restraints weight = 8180.876| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.42 r_work: 0.3703 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6194 Z= 0.164 Angle : 0.520 8.926 8956 Z= 0.299 Chirality : 0.037 0.159 1067 Planarity : 0.005 0.063 666 Dihedral : 23.769 91.724 2294 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.72 % Allowed : 18.58 % 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: 0.65 (0.44), residues: 375 helix: 1.98 (0.38), residues: 186 sheet: -1.20 (0.68), residues: 55 loop : -1.06 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.028 0.002 TYR A 309 PHE 0.022 0.002 PHE A 118 TRP 0.005 0.001 TRP A 300 HIS 0.006 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 6194) covalent geometry : angle 0.51985 / 0.30 ( 8956) hydrogen bonds : bond 0.06895 / 4.88 ( 272) hydrogen bonds : angle 3.26990 / 2.42 ( 655) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.104 Fit side-chains REVERT: A 76 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7046 (pttp) REVERT: A 304 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7889 (ttp80) REVERT: A 370 ARG cc_start: 0.7154 (mtp180) cc_final: 0.6845 (mtp180) outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.5782 time to fit residues: 37.1796 Evaluate side-chains 61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.0060 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.0050 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.154483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.136500 restraints weight = 8022.870| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.39 r_work: 0.3732 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6194 Z= 0.135 Angle : 0.482 7.074 8956 Z= 0.281 Chirality : 0.035 0.153 1067 Planarity : 0.005 0.061 666 Dihedral : 23.753 93.277 2294 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.02 % Allowed : 18.58 % Favored : 77.40 % 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: 0.74 (0.44), residues: 375 helix: 2.18 (0.38), residues: 186 sheet: -1.24 (0.59), residues: 70 loop : -1.12 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.022 0.002 TYR A 309 PHE 0.029 0.003 PHE A 30 TRP 0.005 0.001 TRP A 300 HIS 0.006 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 ( 6194) covalent geometry : angle 0.48180 / 0.28 ( 8956) hydrogen bonds : bond 0.06357 / 4.53 ( 272) hydrogen bonds : angle 3.17611 / 2.34 ( 655) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.110 Fit side-chains REVERT: A 76 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6965 (pttp) REVERT: A 304 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7875 (ttp80) REVERT: A 370 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6841 (mtp180) outliers start: 13 outliers final: 6 residues processed: 61 average time/residue: 0.5938 time to fit residues: 37.5971 Evaluate side-chains 61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 348 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 0.0010 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 0.0870 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.156349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.138254 restraints weight = 8131.282| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.42 r_work: 0.3755 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6194 Z= 0.120 Angle : 0.466 6.785 8956 Z= 0.271 Chirality : 0.034 0.152 1067 Planarity : 0.005 0.060 666 Dihedral : 23.666 94.875 2294 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.33 % Allowed : 18.27 % Favored : 77.40 % 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: 0.87 (0.44), residues: 375 helix: 2.36 (0.38), residues: 185 sheet: -1.14 (0.59), residues: 70 loop : -1.18 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.020 0.002 TYR A 309 PHE 0.018 0.002 PHE A 93 TRP 0.005 0.001 TRP A 300 HIS 0.005 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 ( 6194) covalent geometry : angle 0.46633 / 0.27 ( 8956) hydrogen bonds : bond 0.05842 / 4.17 ( 272) hydrogen bonds : angle 3.06313 / 2.26 ( 655) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.127 Fit side-chains REVERT: A 76 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6858 (pttp) REVERT: A 83 LEU cc_start: 0.8326 (mp) cc_final: 0.8121 (mm) REVERT: A 304 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7930 (ttp80) REVERT: A 356 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7420 (t) REVERT: A 370 ARG cc_start: 0.7143 (mtp180) cc_final: 0.6832 (mtp180) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.5846 time to fit residues: 36.4897 Evaluate side-chains 65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 356 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.0980 chunk 13 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.156302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.138247 restraints weight = 8126.140| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.41 r_work: 0.3753 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6194 Z= 0.127 Angle : 0.464 7.254 8956 Z= 0.269 Chirality : 0.034 0.154 1067 Planarity : 0.005 0.059 666 Dihedral : 23.644 94.536 2294 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.79 % Allowed : 19.81 % Favored : 77.40 % 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: 0.94 (0.44), residues: 375 helix: 2.41 (0.38), residues: 185 sheet: -1.07 (0.58), residues: 70 loop : -1.18 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.022 0.002 TYR A 309 PHE 0.040 0.003 PHE A 93 TRP 0.004 0.001 TRP A 300 HIS 0.006 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 6194) covalent geometry : angle 0.46358 / 0.27 ( 8956) hydrogen bonds : bond 0.05854 / 4.14 ( 272) hydrogen bonds : angle 3.06262 / 2.25 ( 655) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.087 Fit side-chains REVERT: A 76 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6898 (pttp) REVERT: A 83 LEU cc_start: 0.8357 (mp) cc_final: 0.8150 (mm) REVERT: A 304 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7930 (ttp80) REVERT: A 370 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6830 (mtp180) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.5724 time to fit residues: 34.9904 Evaluate side-chains 62 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 348 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.137884 restraints weight = 7921.029| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.47 r_work: 0.3745 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6194 Z= 0.132 Angle : 0.465 7.176 8956 Z= 0.271 Chirality : 0.034 0.154 1067 Planarity : 0.005 0.057 666 Dihedral : 23.620 94.241 2294 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.41 % Allowed : 19.20 % Favored : 77.40 % 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: 0.87 (0.44), residues: 375 helix: 2.40 (0.38), residues: 185 sheet: -1.04 (0.58), residues: 70 loop : -1.34 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.023 0.002 TYR A 309 PHE 0.018 0.002 PHE A 118 TRP 0.004 0.001 TRP A 300 HIS 0.006 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 6194) covalent geometry : angle 0.46506 / 0.27 ( 8956) hydrogen bonds : bond 0.05866 / 4.12 ( 272) hydrogen bonds : angle 3.06403 / 2.25 ( 655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2327.87 seconds wall clock time: 40 minutes 18.06 seconds (2418.06 seconds total)