Starting phenix.real_space_refine on Tue Aug 4 14:13:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u47_63833/08_2026/9u47_63833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u47_63833/08_2026/9u47_63833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u47_63833/08_2026/9u47_63833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u47_63833/08_2026/9u47_63833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u47_63833/08_2026/9u47_63833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u47_63833/08_2026/9u47_63833.map" } resolution = 3.4 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 436 atoms to isotropic. 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 42 5.49 5 S 18 5.16 5 C 1976 2.51 5 N 588 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 3374 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 896 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 5, 'rna3p': 36} Chain: "A" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2478 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P U B 82 " occ=0.50 ... (18 atoms not shown) pdb=" C6 U B 82 " occ=0.50 Time building chain proxies: 0.78, per 1000 atoms: 0.23 Number of scatterers: 3374 At special positions: 0 Unit cell: (66.4, 82.17, 88.81, 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 18 16.00 P 42 15.00 O 750 8.00 N 588 7.00 C 1976 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: 0.30 Conformation dependent library (CDL) restraints added in 92.1 milliseconds 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 582 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 2 sheets defined 40.3% alpha, 21.4% beta 13 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 63 through 80 Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.040A pdb=" N LEU A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.599A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 removed outlier: 4.581A pdb=" N ALA A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.664A pdb=" N ILE A 277 " --> pdb=" O HIS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.172A pdb=" N LEU A 284 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 316 removed outlier: 5.320A pdb=" N ASP A 307 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 378 through 395 removed outlier: 4.351A pdb=" N TYR A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 145 removed outlier: 6.564A pdb=" N GLY A 92 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR A 118 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP A 94 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 91 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET A 166 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 93 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 296 removed outlier: 6.343A pdb=" N LYS A 359 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY A 356 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 334 " --> pdb=" O GLY A 356 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 0.48 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 466 1.32 - 1.44: 1190 1.44 - 1.57: 1766 1.57 - 1.70: 83 1.70 - 1.83: 26 Bond restraints: 3531 Sorted by residual: bond pdb=" N PRO A 154 " pdb=" CA PRO A 154 " ideal model delta sigma weight residual 1.465 1.426 0.039 1.10e-02 8.26e+03 1.24e+01 bond pdb=" C PRO A 154 " pdb=" O PRO A 154 " ideal model delta sigma weight residual 1.232 1.187 0.044 1.31e-02 5.83e+03 1.13e+01 bond pdb=" C LEU A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.328 1.367 -0.038 1.26e-02 6.30e+03 9.34e+00 bond pdb=" O3' A B 80 " pdb=" P U B 81 " ideal model delta sigma weight residual 1.607 1.642 -0.035 1.20e-02 6.94e+03 8.73e+00 bond pdb=" N7 A B 64 " pdb=" C5 A B 64 " ideal model delta sigma weight residual 1.388 1.371 0.017 6.00e-03 2.78e+04 8.50e+00 ... (remaining 3526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 4582 1.66 - 3.32: 315 3.32 - 4.98: 53 4.98 - 6.64: 11 6.64 - 8.31: 3 Bond angle restraints: 4964 Sorted by residual: angle pdb=" O5' U B 58 " pdb=" C5' U B 58 " pdb=" C4' U B 58 " ideal model delta sigma weight residual 109.40 114.41 -5.01 8.00e-01 1.56e+00 3.92e+01 angle pdb=" CA TRP A 337 " pdb=" C TRP A 337 " pdb=" O TRP A 337 " ideal model delta sigma weight residual 121.78 116.43 5.35 1.12e+00 7.97e-01 2.28e+01 angle pdb=" N PRO A 154 " pdb=" CA PRO A 154 " pdb=" CB PRO A 154 " ideal model delta sigma weight residual 103.15 109.21 -6.06 1.29e+00 6.01e-01 2.20e+01 angle pdb=" C ALA A 341 " pdb=" N ARG A 342 " pdb=" CA ARG A 342 " ideal model delta sigma weight residual 120.63 114.91 5.72 1.36e+00 5.41e-01 1.77e+01 angle pdb=" N TRP A 337 " pdb=" CA TRP A 337 " pdb=" C TRP A 337 " ideal model delta sigma weight residual 110.06 116.00 -5.94 1.43e+00 4.89e-01 1.73e+01 ... (remaining 4959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 1943 14.97 - 29.93: 109 29.93 - 44.90: 54 44.90 - 59.87: 41 59.87 - 74.83: 35 Dihedral angle restraints: 2182 sinusoidal: 1282 harmonic: 900 Sorted by residual: dihedral pdb=" CA LEU A 354 " pdb=" C LEU A 354 " pdb=" N GLU A 355 " pdb=" CA GLU A 355 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA GLN A 268 " pdb=" C GLN A 268 " pdb=" N ALA A 269 " pdb=" CA ALA A 269 " ideal model delta harmonic sigma weight residual -180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" N PRO A 154 " pdb=" C PRO A 154 " pdb=" CA PRO A 154 " pdb=" CB PRO A 154 " ideal model delta harmonic sigma weight residual 115.10 125.83 -10.73 0 2.50e+00 1.60e-01 1.84e+01 ... (remaining 2179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 507 0.095 - 0.190: 71 0.190 - 0.285: 1 0.285 - 0.380: 0 0.380 - 0.475: 1 Chirality restraints: 580 Sorted by residual: chirality pdb=" CA PRO A 154 " pdb=" N PRO A 154 " pdb=" C PRO A 154 " pdb=" CB PRO A 154 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C2' C B 55 " pdb=" C3' C B 55 " pdb=" O2' C B 55 " pdb=" C1' C B 55 " both_signs ideal model delta sigma weight residual False -2.62 -2.81 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" C2' C B 60 " pdb=" C3' C B 60 " pdb=" O2' C B 60 " pdb=" C1' C B 60 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 577 not shown) Planarity restraints: 471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 373 " -0.016 2.00e-02 2.50e+03 1.81e-02 8.23e+00 pdb=" CG TRP A 373 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 373 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 373 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 373 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 373 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 373 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 373 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 373 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 373 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 299 " 0.040 5.00e-02 4.00e+02 5.98e-02 5.71e+00 pdb=" N PRO A 300 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 300 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 300 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 277 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C ILE A 277 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE A 277 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 278 " 0.014 2.00e-02 2.50e+03 ... (remaining 468 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 722 2.79 - 3.31: 2850 3.31 - 3.84: 5961 3.84 - 4.37: 6987 4.37 - 4.90: 10382 Nonbonded interactions: 26902 Sorted by model distance: nonbonded pdb=" OE2 GLU A 203 " pdb=" OG SER A 232 " model vdw 2.256 3.040 nonbonded pdb=" O2' C B 55 " pdb=" NE ARG A 391 " model vdw 2.261 3.120 nonbonded pdb=" O2' C B 79 " pdb=" O4' A B 80 " model vdw 2.270 3.040 nonbonded pdb=" O LEU A 77 " pdb=" OG1 THR A 81 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR A 70 " pdb=" OG1 THR A 224 " model vdw 2.332 3.040 ... (remaining 26897 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=0.50 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.910 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 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 : 0.006 0.063 3531 Z= 0.406 Angle : 0.958 8.306 4964 Z= 0.694 Chirality : 0.062 0.475 580 Planarity : 0.006 0.060 471 Dihedral : 16.671 74.832 1600 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.34 % 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: -2.80 (0.43), residues: 304 helix: -1.72 (0.42), residues: 108 sheet: -0.93 (0.60), residues: 77 loop : -2.48 (0.50), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 271 TYR 0.020 0.004 TYR A 382 PHE 0.021 0.003 PHE A 164 TRP 0.049 0.005 TRP A 373 HIS 0.001 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.41 ( 3531) covalent geometry : angle 0.95806 / 0.69 ( 4964) hydrogen bonds : bond 0.14913 / 17.07 ( 151) hydrogen bonds : angle 7.76636 / 9.72 ( 397) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.102 Fit side-chains REVERT: A 77 LEU cc_start: 0.7823 (tp) cc_final: 0.7468 (tp) REVERT: A 248 TYR cc_start: 0.7545 (p90) cc_final: 0.6877 (p90) REVERT: A 250 ILE cc_start: 0.8093 (mt) cc_final: 0.7828 (tt) REVERT: A 264 CYS cc_start: 0.6421 (p) cc_final: 0.5430 (p) REVERT: A 358 MET cc_start: 0.6750 (ttp) cc_final: 0.6494 (ttt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0705 time to fit residues: 5.8180 Evaluate side-chains 58 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN A 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.200803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.177450 restraints weight = 5844.391| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 3.17 r_work: 0.4207 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4200 r_free = 0.4200 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4200 r_free = 0.4200 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3531 Z= 0.185 Angle : 0.630 6.108 4964 Z= 0.349 Chirality : 0.042 0.158 580 Planarity : 0.005 0.046 471 Dihedral : 19.547 74.139 971 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.43 % Allowed : 10.39 % Favored : 88.17 % 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: -1.54 (0.47), residues: 304 helix: -0.34 (0.47), residues: 116 sheet: -0.76 (0.57), residues: 77 loop : -1.79 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 391 TYR 0.013 0.002 TYR A 111 PHE 0.015 0.002 PHE A 164 TRP 0.030 0.003 TRP A 222 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 3531) covalent geometry : angle 0.62966 / 0.35 ( 4964) hydrogen bonds : bond 0.05947 / 6.24 ( 151) hydrogen bonds : angle 6.16176 / 7.57 ( 397) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.105 Fit side-chains REVERT: A 163 THR cc_start: 0.5928 (p) cc_final: 0.5322 (m) REVERT: A 224 THR cc_start: 0.7493 (p) cc_final: 0.7232 (p) REVERT: A 250 ILE cc_start: 0.8168 (mt) cc_final: 0.7928 (mt) REVERT: A 252 GLU cc_start: 0.5284 (tt0) cc_final: 0.4958 (tt0) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 0.0889 time to fit residues: 6.5324 Evaluate side-chains 60 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 GLN ** A 367 ASN ** 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 = 0.4593 r_free = 0.4593 target = 0.199917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.176563 restraints weight = 5771.981| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 3.16 r_work: 0.4192 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3531 Z= 0.173 Angle : 0.581 6.345 4964 Z= 0.321 Chirality : 0.040 0.143 580 Planarity : 0.005 0.046 471 Dihedral : 19.484 74.247 971 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.87 % Allowed : 8.96 % Favored : 88.17 % 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: -0.92 (0.48), residues: 304 helix: 0.36 (0.48), residues: 116 sheet: -0.69 (0.57), residues: 76 loop : -1.45 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 260 TYR 0.028 0.002 TYR A 382 PHE 0.014 0.001 PHE A 164 TRP 0.014 0.002 TRP A 222 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 3531) covalent geometry : angle 0.58052 / 0.32 ( 4964) hydrogen bonds : bond 0.05154 / 5.55 ( 151) hydrogen bonds : angle 6.01722 / 7.48 ( 397) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.108 Fit side-chains REVERT: A 163 THR cc_start: 0.5878 (p) cc_final: 0.5295 (m) REVERT: A 224 THR cc_start: 0.7455 (p) cc_final: 0.7218 (p) REVERT: A 250 ILE cc_start: 0.8217 (mt) cc_final: 0.7965 (mt) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.0755 time to fit residues: 5.5816 Evaluate side-chains 60 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN ** A 367 ASN ** 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 = 0.4559 r_free = 0.4559 target = 0.196739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.173280 restraints weight = 5621.026| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.11 r_work: 0.4148 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3531 Z= 0.199 Angle : 0.596 5.229 4964 Z= 0.329 Chirality : 0.041 0.140 580 Planarity : 0.005 0.044 471 Dihedral : 19.632 74.153 971 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.51 % Allowed : 9.68 % Favored : 87.81 % 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: -0.60 (0.49), residues: 304 helix: 0.60 (0.50), residues: 116 sheet: -0.50 (0.59), residues: 76 loop : -1.27 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 391 TYR 0.039 0.003 TYR A 382 PHE 0.019 0.002 PHE A 164 TRP 0.009 0.002 TRP A 265 HIS 0.003 0.002 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 ( 3531) covalent geometry : angle 0.59569 / 0.33 ( 4964) hydrogen bonds : bond 0.05080 / 5.50 ( 151) hydrogen bonds : angle 5.88554 / 7.44 ( 397) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.101 Fit side-chains REVERT: A 163 THR cc_start: 0.6262 (p) cc_final: 0.5722 (m) REVERT: A 250 ILE cc_start: 0.8274 (mt) cc_final: 0.8032 (mt) REVERT: A 252 GLU cc_start: 0.5768 (tt0) cc_final: 0.5548 (tt0) REVERT: A 342 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6624 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.0758 time to fit residues: 5.7112 Evaluate side-chains 64 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 7 optimal weight: 0.1980 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.199661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.176002 restraints weight = 5768.267| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 3.24 r_work: 0.4166 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4166 r_free = 0.4166 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4166 r_free = 0.4166 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3531 Z= 0.136 Angle : 0.549 7.014 4964 Z= 0.304 Chirality : 0.040 0.266 580 Planarity : 0.005 0.043 471 Dihedral : 19.575 74.085 971 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.87 % Allowed : 11.11 % Favored : 86.02 % 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: -0.14 (0.50), residues: 304 helix: 1.02 (0.52), residues: 114 sheet: -0.32 (0.61), residues: 76 loop : -0.97 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.035 0.002 TYR A 382 PHE 0.016 0.001 PHE A 164 TRP 0.013 0.001 TRP A 265 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 3531) covalent geometry : angle 0.54943 / 0.30 ( 4964) hydrogen bonds : bond 0.04220 / 4.59 ( 151) hydrogen bonds : angle 5.76896 / 7.37 ( 397) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.097 Fit side-chains REVERT: A 240 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7735 (mt) REVERT: A 250 ILE cc_start: 0.8248 (mt) cc_final: 0.8007 (mt) REVERT: A 271 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.7273 (mmt-90) REVERT: A 342 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6540 (mtm-85) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.0773 time to fit residues: 5.7850 Evaluate side-chains 63 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.197269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.173609 restraints weight = 5780.414| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.23 r_work: 0.4141 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4150 r_free = 0.4150 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4150 r_free = 0.4150 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3531 Z= 0.198 Angle : 0.617 6.962 4964 Z= 0.342 Chirality : 0.042 0.222 580 Planarity : 0.005 0.047 471 Dihedral : 19.614 74.108 971 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.51 % Allowed : 11.83 % Favored : 85.66 % 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: -0.28 (0.49), residues: 304 helix: 0.87 (0.51), residues: 114 sheet: -0.30 (0.62), residues: 76 loop : -1.09 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 146 TYR 0.042 0.003 TYR A 382 PHE 0.014 0.001 PHE A 164 TRP 0.008 0.001 TRP A 265 HIS 0.004 0.002 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 ( 3531) covalent geometry : angle 0.61724 / 0.34 ( 4964) hydrogen bonds : bond 0.04863 / 5.29 ( 151) hydrogen bonds : angle 5.79935 / 7.48 ( 397) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.071 Fit side-chains REVERT: A 240 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7745 (mt) REVERT: A 250 ILE cc_start: 0.8248 (mt) cc_final: 0.8023 (mt) REVERT: A 342 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6697 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 0.0875 time to fit residues: 6.2788 Evaluate side-chains 61 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.195842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.171631 restraints weight = 5794.483| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 3.35 r_work: 0.4115 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3531 Z= 0.217 Angle : 0.636 6.253 4964 Z= 0.355 Chirality : 0.043 0.184 580 Planarity : 0.005 0.047 471 Dihedral : 19.716 74.102 971 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.23 % Allowed : 12.90 % Favored : 83.87 % 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: -0.40 (0.49), residues: 304 helix: 0.72 (0.50), residues: 114 sheet: -0.52 (0.62), residues: 78 loop : -0.98 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 260 TYR 0.049 0.003 TYR A 382 PHE 0.025 0.002 PHE A 125 TRP 0.008 0.002 TRP A 337 HIS 0.005 0.002 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 ( 3531) covalent geometry : angle 0.63552 / 0.36 ( 4964) hydrogen bonds : bond 0.05057 / 5.54 ( 151) hydrogen bonds : angle 5.82633 / 7.56 ( 397) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.103 Fit side-chains REVERT: A 125 PHE cc_start: 0.2523 (OUTLIER) cc_final: 0.2286 (t80) REVERT: A 239 LYS cc_start: 0.6730 (tptt) cc_final: 0.6519 (tptt) REVERT: A 240 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7690 (mt) REVERT: A 250 ILE cc_start: 0.8332 (mt) cc_final: 0.8105 (mt) REVERT: A 342 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6758 (mtm-85) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.0807 time to fit residues: 5.8108 Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 10 optimal weight: 0.0370 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.199268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.177458 restraints weight = 5729.016| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 3.01 r_work: 0.4159 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4177 r_free = 0.4177 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4177 r_free = 0.4177 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3531 Z= 0.158 Angle : 0.591 6.499 4964 Z= 0.328 Chirality : 0.041 0.164 580 Planarity : 0.005 0.046 471 Dihedral : 19.723 74.113 971 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.51 % Allowed : 13.98 % Favored : 83.51 % 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: -0.22 (0.50), residues: 304 helix: 0.84 (0.50), residues: 115 sheet: -0.53 (0.61), residues: 78 loop : -0.74 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 271 TYR 0.052 0.003 TYR A 382 PHE 0.016 0.002 PHE A 164 TRP 0.012 0.002 TRP A 265 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 3531) covalent geometry : angle 0.59118 / 0.33 ( 4964) hydrogen bonds : bond 0.04386 / 4.82 ( 151) hydrogen bonds : angle 5.71475 / 7.33 ( 397) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.062 Fit side-chains REVERT: A 125 PHE cc_start: 0.2372 (OUTLIER) cc_final: 0.2138 (t80) REVERT: A 240 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7661 (mt) REVERT: A 250 ILE cc_start: 0.8334 (mt) cc_final: 0.8099 (mt) REVERT: A 271 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.7314 (mmt-90) REVERT: A 342 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6962 (mtm-85) outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 0.0696 time to fit residues: 4.8903 Evaluate side-chains 60 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.0570 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.201123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.179501 restraints weight = 5703.106| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 3.00 r_work: 0.4178 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3531 Z= 0.135 Angle : 0.559 5.656 4964 Z= 0.312 Chirality : 0.040 0.179 580 Planarity : 0.005 0.046 471 Dihedral : 19.636 74.100 971 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.87 % Allowed : 12.54 % Favored : 84.59 % 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: -0.03 (0.50), residues: 304 helix: 1.11 (0.51), residues: 115 sheet: -0.73 (0.59), residues: 80 loop : -0.49 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 271 TYR 0.041 0.003 TYR A 382 PHE 0.016 0.002 PHE A 125 TRP 0.015 0.002 TRP A 265 HIS 0.001 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 3531) covalent geometry : angle 0.55903 / 0.31 ( 4964) hydrogen bonds : bond 0.03895 / 4.29 ( 151) hydrogen bonds : angle 5.56642 / 7.08 ( 397) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.062 Fit side-chains REVERT: A 240 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7624 (mt) REVERT: A 250 ILE cc_start: 0.8324 (mt) cc_final: 0.8084 (mt) REVERT: A 342 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6883 (mtm-85) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.0695 time to fit residues: 4.9581 Evaluate side-chains 62 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.0040 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 20 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.201247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.179764 restraints weight = 5701.950| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.98 r_work: 0.4192 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4197 r_free = 0.4197 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4197 r_free = 0.4197 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3531 Z= 0.127 Angle : 0.560 6.489 4964 Z= 0.312 Chirality : 0.039 0.183 580 Planarity : 0.006 0.064 471 Dihedral : 19.567 74.004 971 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.58 % Allowed : 12.90 % Favored : 83.51 % 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: 0.15 (0.50), residues: 304 helix: 1.18 (0.51), residues: 115 sheet: -0.33 (0.61), residues: 78 loop : -0.58 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 271 TYR 0.059 0.003 TYR A 382 PHE 0.012 0.001 PHE A 125 TRP 0.015 0.002 TRP A 265 HIS 0.001 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 3531) covalent geometry : angle 0.56030 / 0.31 ( 4964) hydrogen bonds : bond 0.03760 / 4.14 ( 151) hydrogen bonds : angle 5.49697 / 6.94 ( 397) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.101 Fit side-chains REVERT: A 74 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 159 MET cc_start: 0.6197 (mpp) cc_final: 0.5737 (mpp) REVERT: A 240 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7609 (mt) REVERT: A 250 ILE cc_start: 0.8272 (mt) cc_final: 0.8031 (mt) REVERT: A 342 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6889 (mtm-85) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.0726 time to fit residues: 5.1336 Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 386 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 6 optimal weight: 0.0070 chunk 30 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.196376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.173662 restraints weight = 5646.281| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 3.22 r_work: 0.4140 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4150 r_free = 0.4150 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4150 r_free = 0.4150 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3531 Z= 0.164 Angle : 0.577 5.455 4964 Z= 0.322 Chirality : 0.040 0.166 580 Planarity : 0.006 0.070 471 Dihedral : 19.609 73.955 971 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.23 % Allowed : 13.62 % Favored : 83.15 % 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: 0.03 (0.50), residues: 304 helix: 1.09 (0.50), residues: 115 sheet: -0.53 (0.60), residues: 80 loop : -0.55 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 271 TYR 0.052 0.003 TYR A 382 PHE 0.016 0.002 PHE A 125 TRP 0.008 0.002 TRP A 222 HIS 0.005 0.002 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 3531) covalent geometry : angle 0.57690 / 0.32 ( 4964) hydrogen bonds : bond 0.04295 / 4.77 ( 151) hydrogen bonds : angle 5.52915 / 6.98 ( 397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1029.71 seconds wall clock time: 18 minutes 21.65 seconds (1101.65 seconds total)