Starting phenix.real_space_refine on Thu Jul 2 00:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u48_63834/07_2026/9u48_63834.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u48_63834/07_2026/9u48_63834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u48_63834/07_2026/9u48_63834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u48_63834/07_2026/9u48_63834.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u48_63834/07_2026/9u48_63834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u48_63834/07_2026/9u48_63834.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 1301 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 49 5.49 5 S 21 5.16 5 C 2206 2.51 5 N 666 2.21 5 O 848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3790 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2712 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 320} Chain breaks: 1 Chain: "B" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1051 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 10, 'rna3p': 38} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" P C B 36 " occ=0.50 ... (18 atoms not shown) pdb=" C6 C B 36 " occ=0.50 residue: pdb=" P U B 82 " occ=0.50 ... (18 atoms not shown) pdb=" C6 U B 82 " occ=0.50 residue: pdb=" P G B 83 " occ=0.50 ... (21 atoms not shown) pdb=" C4 G B 83 " occ=0.50 Time building chain proxies: 0.97, per 1000 atoms: 0.26 Number of scatterers: 3790 At special positions: 0 Unit cell: (59.76, 69.72, 90.47, 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 21 16.00 P 49 15.00 O 848 8.00 N 666 7.00 C 2206 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: 0.29 Conformation dependent library (CDL) restraints added in 104.5 milliseconds 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 638 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 37.3% alpha, 0.0% beta 13 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 65 through 79 Processing helix chain 'A' and resid 102 through 111 removed outlier: 3.697A pdb=" N MET A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.769A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Proline residue: A 234 - end of helix Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 300 through 317 removed outlier: 6.744A pdb=" N ASP A 307 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASP A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 379 through 397 removed outlier: 3.617A pdb=" N ASN A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 0.53 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1019 1.34 - 1.46: 1028 1.46 - 1.57: 1801 1.57 - 1.69: 97 1.69 - 1.81: 32 Bond restraints: 3977 Sorted by residual: bond pdb=" C TYR A 70 " pdb=" N ILE A 71 " ideal model delta sigma weight residual 1.334 1.267 0.068 1.26e-02 6.30e+03 2.88e+01 bond pdb=" O3' G B 43 " pdb=" P A B 44 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.50e-02 4.44e+03 8.49e+00 bond pdb=" O3' A B 35 " pdb=" P C B 36 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.50e-02 4.44e+03 8.46e+00 bond pdb=" N3 C B 55 " pdb=" C4 C B 55 " ideal model delta sigma weight residual 1.335 1.317 0.018 7.00e-03 2.04e+04 6.34e+00 bond pdb=" N THR A 81 " pdb=" CA THR A 81 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.00e-02 1.00e+04 5.12e+00 ... (remaining 3972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 5402 1.77 - 3.54: 177 3.54 - 5.32: 21 5.32 - 7.09: 7 7.09 - 8.86: 2 Bond angle restraints: 5609 Sorted by residual: angle pdb=" O3' A B 35 " pdb=" C3' A B 35 " pdb=" C2' A B 35 " ideal model delta sigma weight residual 109.50 118.36 -8.86 1.50e+00 4.44e-01 3.49e+01 angle pdb=" O3' G B 43 " pdb=" C3' G B 43 " pdb=" C2' G B 43 " ideal model delta sigma weight residual 113.70 107.14 6.56 1.50e+00 4.44e-01 1.92e+01 angle pdb=" C4' G B 43 " pdb=" C3' G B 43 " pdb=" O3' G B 43 " ideal model delta sigma weight residual 113.00 119.17 -6.17 1.50e+00 4.44e-01 1.69e+01 angle pdb=" C1' G B 75 " pdb=" N9 G B 75 " pdb=" C4 G B 75 " ideal model delta sigma weight residual 126.50 131.76 -5.26 1.30e+00 5.92e-01 1.64e+01 angle pdb=" C1' G B 75 " pdb=" N9 G B 75 " pdb=" C8 G B 75 " ideal model delta sigma weight residual 127.00 122.17 4.83 1.30e+00 5.92e-01 1.38e+01 ... (remaining 5604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 2282 33.44 - 66.87: 164 66.87 - 100.31: 24 100.31 - 133.75: 1 133.75 - 167.18: 1 Dihedral angle restraints: 2472 sinusoidal: 1488 harmonic: 984 Sorted by residual: dihedral pdb=" C5' A B 35 " pdb=" C4' A B 35 " pdb=" C3' A B 35 " pdb=" O3' A B 35 " ideal model delta sinusoidal sigma weight residual 147.00 96.14 50.86 1 8.00e+00 1.56e-02 5.53e+01 dihedral pdb=" O4' A B 35 " pdb=" C4' A B 35 " pdb=" C3' A B 35 " pdb=" C2' A B 35 " ideal model delta sinusoidal sigma weight residual 24.00 -10.65 34.65 1 8.00e+00 1.56e-02 2.66e+01 dihedral pdb=" C3' A B 35 " pdb=" C4' A B 35 " pdb=" O4' A B 35 " pdb=" C1' A B 35 " ideal model delta sinusoidal sigma weight residual -2.00 27.76 -29.76 1 8.00e+00 1.56e-02 1.98e+01 ... (remaining 2469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 622 0.106 - 0.213: 29 0.213 - 0.319: 0 0.319 - 0.425: 0 0.425 - 0.531: 1 Chirality restraints: 652 Sorted by residual: chirality pdb=" C3' A B 35 " pdb=" C4' A B 35 " pdb=" O3' A B 35 " pdb=" C2' A B 35 " both_signs ideal model delta sigma weight residual False -2.74 -2.21 -0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CA SAM A 401 " pdb=" N SAM A 401 " pdb=" C SAM A 401 " pdb=" CB SAM A 401 " both_signs ideal model delta sigma weight residual False 2.45 2.64 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CA PRO A 300 " pdb=" N PRO A 300 " pdb=" C PRO A 300 " pdb=" CB PRO A 300 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 649 not shown) Planarity restraints: 527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 70 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C TYR A 70 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR A 70 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 71 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 43 " 0.026 2.00e-02 2.50e+03 1.21e-02 4.37e+00 pdb=" N9 G B 43 " -0.029 2.00e-02 2.50e+03 pdb=" C8 G B 43 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G B 43 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 43 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G B 43 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 43 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G B 43 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B 43 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 43 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 43 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G B 43 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 233 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 234 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.029 5.00e-02 4.00e+02 ... (remaining 524 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 483 2.74 - 3.28: 3642 3.28 - 3.82: 6851 3.82 - 4.36: 8037 4.36 - 4.90: 12493 Nonbonded interactions: 31506 Sorted by model distance: nonbonded pdb=" O LEU A 211 " pdb=" NZ LYS A 215 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR A 172 " pdb=" O2' C B 36 " model vdw 2.238 3.040 nonbonded pdb=" NE ARG A 89 " pdb=" OD2 ASP A 114 " model vdw 2.259 3.120 nonbonded pdb=" O ARG A 217 " pdb=" OH TYR A 223 " model vdw 2.271 3.040 nonbonded pdb=" NZ LYS A 257 " pdb=" OP2 A B 39 " model vdw 2.295 3.120 ... (remaining 31501 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.730 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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 0.068 3977 Z= 0.366 Angle : 0.754 8.861 5609 Z= 0.531 Chirality : 0.051 0.531 652 Planarity : 0.005 0.052 527 Dihedral : 20.562 167.183 1834 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: -1.25 (0.48), residues: 331 helix: 0.56 (0.50), residues: 122 sheet: -1.43 (0.59), residues: 75 loop : -1.70 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 260 TYR 0.017 0.002 TYR A 70 PHE 0.025 0.002 PHE A 125 TRP 0.014 0.002 TRP A 265 HIS 0.002 0.000 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.37 ( 3977) covalent geometry : angle 0.75352 / 0.53 ( 5609) hydrogen bonds : bond 0.09284 / 6.43 ( 104) hydrogen bonds : angle 5.40376 / 3.99 ( 268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.7659 (mt) cc_final: 0.7431 (mt) REVERT: A 297 THR cc_start: 0.7431 (t) cc_final: 0.7195 (m) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.6670 time to fit residues: 41.7454 Evaluate side-chains 56 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3278 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.183592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.155792 restraints weight = 5222.481| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.15 r_work: 0.3861 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3977 Z= 0.156 Angle : 0.588 6.071 5609 Z= 0.325 Chirality : 0.042 0.202 652 Planarity : 0.005 0.047 527 Dihedral : 22.211 140.266 1139 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.98 % Allowed : 11.44 % Favored : 87.58 % 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: -1.18 (0.48), residues: 331 helix: 0.66 (0.50), residues: 126 sheet: -1.67 (0.57), residues: 77 loop : -1.57 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 146 TYR 0.014 0.002 TYR A 111 PHE 0.019 0.002 PHE A 178 TRP 0.009 0.002 TRP A 265 HIS 0.001 0.000 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 3977) covalent geometry : angle 0.58796 / 0.32 ( 5609) hydrogen bonds : bond 0.05838 / 3.84 ( 104) hydrogen bonds : angle 4.36846 / 3.08 ( 268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.7839 (mt) cc_final: 0.7602 (mt) REVERT: A 270 MET cc_start: 0.7634 (mmp) cc_final: 0.7270 (mpp) REVERT: A 297 THR cc_start: 0.7466 (t) cc_final: 0.7263 (m) outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 0.6118 time to fit residues: 38.3270 Evaluate side-chains 60 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 24 optimal weight: 0.3980 chunk 3 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.182392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.154543 restraints weight = 5093.154| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.18 r_work: 0.3857 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3977 Z= 0.171 Angle : 0.562 6.639 5609 Z= 0.302 Chirality : 0.040 0.156 652 Planarity : 0.004 0.046 527 Dihedral : 21.677 113.837 1139 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.63 % Allowed : 16.34 % Favored : 82.03 % 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: -1.11 (0.48), residues: 331 helix: 0.71 (0.49), residues: 125 sheet: -1.56 (0.58), residues: 77 loop : -1.56 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 260 TYR 0.008 0.002 TYR A 248 PHE 0.020 0.002 PHE A 178 TRP 0.009 0.002 TRP A 265 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 3977) covalent geometry : angle 0.56198 / 0.30 ( 5609) hydrogen bonds : bond 0.05687 / 3.99 ( 104) hydrogen bonds : angle 4.23849 / 2.92 ( 268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6283 (mm-30) REVERT: A 263 ILE cc_start: 0.7830 (mt) cc_final: 0.7586 (mt) REVERT: A 270 MET cc_start: 0.7634 (mmp) cc_final: 0.7266 (mpp) REVERT: A 285 SER cc_start: 0.8643 (t) cc_final: 0.8232 (m) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.6578 time to fit residues: 39.0757 Evaluate side-chains 59 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 275 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 0.2980 chunk 10 optimal weight: 0.0970 chunk 4 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 overall best weight: 0.1936 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.184823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.157037 restraints weight = 5104.360| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.18 r_work: 0.3893 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (13 function evaluations) r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3977 Z= 0.114 Angle : 0.517 6.603 5609 Z= 0.278 Chirality : 0.038 0.135 652 Planarity : 0.004 0.051 527 Dihedral : 21.391 103.402 1139 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.59 % Allowed : 17.97 % Favored : 78.43 % 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: -0.88 (0.48), residues: 331 helix: 0.87 (0.49), residues: 125 sheet: -1.36 (0.57), residues: 77 loop : -1.46 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.008 0.001 TYR A 113 PHE 0.020 0.002 PHE A 206 TRP 0.007 0.001 TRP A 265 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 3977) covalent geometry : angle 0.51669 / 0.28 ( 5609) hydrogen bonds : bond 0.05018 / 3.57 ( 104) hydrogen bonds : angle 4.01775 / 2.77 ( 268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6304 (mm-30) REVERT: A 263 ILE cc_start: 0.7780 (mt) cc_final: 0.7554 (mt) REVERT: A 270 MET cc_start: 0.7656 (mmp) cc_final: 0.7314 (mpp) REVERT: A 285 SER cc_start: 0.8629 (t) cc_final: 0.8236 (m) REVERT: A 286 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7812 (ttmm) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.5883 time to fit residues: 35.6658 Evaluate side-chains 63 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 303 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.181923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155249 restraints weight = 5077.768| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.99 r_work: 0.3879 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3977 Z= 0.180 Angle : 0.543 6.672 5609 Z= 0.291 Chirality : 0.040 0.150 652 Planarity : 0.004 0.048 527 Dihedral : 21.222 104.467 1139 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.27 % Allowed : 18.63 % Favored : 78.10 % 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: -0.84 (0.48), residues: 331 helix: 0.91 (0.49), residues: 125 sheet: -1.34 (0.56), residues: 77 loop : -1.45 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.009 0.001 TYR A 248 PHE 0.020 0.003 PHE A 125 TRP 0.007 0.002 TRP A 265 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 3977) covalent geometry : angle 0.54329 / 0.29 ( 5609) hydrogen bonds : bond 0.05512 / 4.27 ( 104) hydrogen bonds : angle 4.10405 / 2.81 ( 268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.7946 (mpt) cc_final: 0.7717 (mpt) REVERT: A 138 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6144 (mm-30) REVERT: A 239 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7361 (mtpt) REVERT: A 263 ILE cc_start: 0.7804 (mt) cc_final: 0.7581 (mt) REVERT: A 270 MET cc_start: 0.7625 (mmp) cc_final: 0.7310 (mpp) REVERT: A 285 SER cc_start: 0.8616 (t) cc_final: 0.8251 (m) REVERT: A 286 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7768 (ttpp) REVERT: A 312 LYS cc_start: 0.7254 (mmtt) cc_final: 0.6985 (mmtt) REVERT: A 323 LYS cc_start: 0.7430 (tptt) cc_final: 0.7135 (tmtt) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.6284 time to fit residues: 39.3313 Evaluate side-chains 64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.181823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154331 restraints weight = 5198.126| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.12 r_work: 0.3860 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (18 function evaluations) r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3977 Z= 0.182 Angle : 0.554 6.823 5609 Z= 0.295 Chirality : 0.040 0.169 652 Planarity : 0.005 0.060 527 Dihedral : 21.123 103.831 1139 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.27 % Allowed : 19.28 % Favored : 77.45 % 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: -0.86 (0.48), residues: 331 helix: 0.90 (0.49), residues: 125 sheet: -1.35 (0.57), residues: 77 loop : -1.47 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 339 TYR 0.009 0.001 TYR A 248 PHE 0.019 0.002 PHE A 125 TRP 0.009 0.002 TRP A 265 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 3977) covalent geometry : angle 0.55391 / 0.29 ( 5609) hydrogen bonds : bond 0.05561 / 4.27 ( 104) hydrogen bonds : angle 4.10471 / 2.80 ( 268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8261 (mp) cc_final: 0.8049 (mm) REVERT: A 138 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6172 (mm-30) REVERT: A 263 ILE cc_start: 0.7842 (mt) cc_final: 0.7610 (mt) REVERT: A 270 MET cc_start: 0.7639 (mmp) cc_final: 0.7299 (mpp) REVERT: A 285 SER cc_start: 0.8625 (t) cc_final: 0.8272 (m) REVERT: A 286 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7877 (ttmm) REVERT: A 312 LYS cc_start: 0.7298 (mmtt) cc_final: 0.7028 (mmtt) REVERT: A 323 LYS cc_start: 0.7438 (tptt) cc_final: 0.7098 (tmtt) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.6044 time to fit residues: 38.4608 Evaluate side-chains 67 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 0.0370 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.183241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.156053 restraints weight = 5202.430| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.04 r_work: 0.3871 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (21 function evaluations) r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3977 Z= 0.165 Angle : 0.531 6.913 5609 Z= 0.284 Chirality : 0.039 0.144 652 Planarity : 0.004 0.048 527 Dihedral : 21.032 103.062 1139 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.92 % Allowed : 19.61 % Favored : 76.47 % 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: -0.79 (0.48), residues: 331 helix: 0.95 (0.49), residues: 125 sheet: -1.33 (0.57), residues: 77 loop : -1.40 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 109 TYR 0.008 0.001 TYR A 248 PHE 0.017 0.002 PHE A 125 TRP 0.009 0.002 TRP A 265 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 3977) covalent geometry : angle 0.53074 / 0.28 ( 5609) hydrogen bonds : bond 0.05465 / 4.17 ( 104) hydrogen bonds : angle 4.09694 / 2.78 ( 268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6147 (mm-30) REVERT: A 270 MET cc_start: 0.7597 (mmp) cc_final: 0.7272 (mpp) REVERT: A 285 SER cc_start: 0.8598 (t) cc_final: 0.8250 (m) REVERT: A 286 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7848 (ttmm) REVERT: A 312 LYS cc_start: 0.7362 (mmtt) cc_final: 0.7076 (mmtt) REVERT: A 323 LYS cc_start: 0.7452 (tptt) cc_final: 0.7147 (tmtt) outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.5972 time to fit residues: 38.6413 Evaluate side-chains 67 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.0040 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 26 optimal weight: 0.4980 chunk 7 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.3190 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.184798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.156909 restraints weight = 5125.679| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.11 r_work: 0.3886 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3977 Z= 0.139 Angle : 0.542 7.829 5609 Z= 0.288 Chirality : 0.038 0.141 652 Planarity : 0.004 0.049 527 Dihedral : 20.964 102.053 1139 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.59 % Allowed : 19.93 % Favored : 76.47 % 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: -0.78 (0.49), residues: 331 helix: 0.93 (0.50), residues: 125 sheet: -1.32 (0.58), residues: 77 loop : -1.36 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.006 0.001 TYR A 113 PHE 0.016 0.002 PHE A 178 TRP 0.009 0.002 TRP A 265 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 3977) covalent geometry : angle 0.54248 / 0.29 ( 5609) hydrogen bonds : bond 0.05207 / 3.93 ( 104) hydrogen bonds : angle 4.12093 / 2.81 ( 268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 SER cc_start: 0.6814 (OUTLIER) cc_final: 0.6546 (m) REVERT: A 138 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6267 (mm-30) REVERT: A 270 MET cc_start: 0.7598 (mmp) cc_final: 0.7284 (mpp) REVERT: A 285 SER cc_start: 0.8598 (t) cc_final: 0.8255 (m) REVERT: A 286 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7891 (ttmm) REVERT: A 312 LYS cc_start: 0.7334 (mmtt) cc_final: 0.7081 (mmtt) REVERT: A 323 LYS cc_start: 0.7404 (tptt) cc_final: 0.7147 (tmtt) outliers start: 11 outliers final: 7 residues processed: 60 average time/residue: 0.5579 time to fit residues: 34.2874 Evaluate side-chains 65 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.0570 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.184587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.157546 restraints weight = 5073.248| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.01 r_work: 0.3897 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3977 Z= 0.142 Angle : 0.545 9.550 5609 Z= 0.282 Chirality : 0.038 0.135 652 Planarity : 0.004 0.048 527 Dihedral : 20.877 101.881 1139 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.59 % Allowed : 19.93 % Favored : 76.47 % 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 (0.49), residues: 331 helix: 0.96 (0.50), residues: 125 sheet: -1.35 (0.59), residues: 77 loop : -1.28 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.006 0.001 TYR A 113 PHE 0.016 0.002 PHE A 178 TRP 0.007 0.002 TRP A 265 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 3977) covalent geometry : angle 0.54541 / 0.28 ( 5609) hydrogen bonds : bond 0.05251 / 4.04 ( 104) hydrogen bonds : angle 4.11214 / 2.78 ( 268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 SER cc_start: 0.6783 (OUTLIER) cc_final: 0.6521 (m) REVERT: A 138 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6111 (mm-30) REVERT: A 270 MET cc_start: 0.7567 (mmp) cc_final: 0.7247 (mpp) REVERT: A 285 SER cc_start: 0.8588 (t) cc_final: 0.8246 (m) REVERT: A 286 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7881 (ttmm) REVERT: A 312 LYS cc_start: 0.7341 (mmtt) cc_final: 0.7068 (mmtt) REVERT: A 323 LYS cc_start: 0.7490 (tptt) cc_final: 0.7211 (tmtt) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.6910 time to fit residues: 41.9020 Evaluate side-chains 66 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.182297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.153869 restraints weight = 5127.485| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.15 r_work: 0.3843 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3977 Z= 0.248 Angle : 0.628 9.339 5609 Z= 0.327 Chirality : 0.043 0.178 652 Planarity : 0.005 0.055 527 Dihedral : 20.826 104.541 1139 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.61 % Allowed : 20.92 % Favored : 76.47 % 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: -0.88 (0.48), residues: 331 helix: 0.85 (0.50), residues: 123 sheet: -1.57 (0.57), residues: 79 loop : -1.23 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.013 0.002 TYR A 248 PHE 0.024 0.003 PHE A 125 TRP 0.009 0.003 TRP A 337 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 ( 3977) covalent geometry : angle 0.62768 / 0.33 ( 5609) hydrogen bonds : bond 0.06285 / 5.03 ( 104) hydrogen bonds : angle 4.28734 / 2.89 ( 268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6116 (mm-30) REVERT: A 270 MET cc_start: 0.7644 (mmp) cc_final: 0.7289 (mpp) REVERT: A 285 SER cc_start: 0.8637 (t) cc_final: 0.8266 (m) REVERT: A 286 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7863 (ttmm) REVERT: A 312 LYS cc_start: 0.7415 (mmtt) cc_final: 0.7132 (mmtt) REVERT: A 323 LYS cc_start: 0.7518 (tptt) cc_final: 0.7175 (tmtt) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.6256 time to fit residues: 38.5435 Evaluate side-chains 64 residues out of total 306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 336 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.0060 chunk 0 optimal weight: 4.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.183825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.155959 restraints weight = 5121.258| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.09 r_work: 0.3873 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3872 r_free = 0.3872 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3872 r_free = 0.3872 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3977 Z= 0.168 Angle : 0.568 10.175 5609 Z= 0.298 Chirality : 0.039 0.151 652 Planarity : 0.004 0.050 527 Dihedral : 20.784 102.963 1139 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.29 % Allowed : 21.24 % Favored : 76.47 % 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: -0.89 (0.49), residues: 331 helix: 0.85 (0.50), residues: 124 sheet: -1.64 (0.57), residues: 79 loop : -1.19 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 146 TYR 0.007 0.001 TYR A 248 PHE 0.017 0.002 PHE A 206 TRP 0.008 0.002 TRP A 265 HIS 0.001 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 3977) covalent geometry : angle 0.56763 / 0.30 ( 5609) hydrogen bonds : bond 0.05654 / 4.27 ( 104) hydrogen bonds : angle 4.19088 / 2.82 ( 268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1460.48 seconds wall clock time: 25 minutes 36.56 seconds (1536.56 seconds total)