Starting phenix.real_space_refine on Wed Mar 12 03:29:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzu_26918/03_2025/7uzu_26918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzu_26918/03_2025/7uzu_26918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uzu_26918/03_2025/7uzu_26918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzu_26918/03_2025/7uzu_26918.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzu_26918/03_2025/7uzu_26918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzu_26918/03_2025/7uzu_26918.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.283 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2286 2.51 5 N 677 2.21 5 O 766 1.98 5 H 3655 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7399 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 6920 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 18, 'TRANS': 432} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 399 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 78 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Conformer: "B" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O AHOH A1933 " occ=0.71 pdb=" O BHOH A1933 " occ=0.29 Time building chain proxies: 4.42, per 1000 atoms: 0.60 Number of scatterers: 7399 At special positions: 0 Unit cell: (94.62, 109.145, 59.345, 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 15 16.00 O 766 8.00 N 677 7.00 C 2286 6.00 H 3655 1.00 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: 1.91 Conformation dependent library (CDL) restraints added in 678.6 milliseconds 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 64.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 274 through 282 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 439 through 448 Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'W' and resid 4 through 7 Processing helix chain 'W' and resid 8 through 17 Processing helix chain 'W' and resid 18 through 22 191 hydrogen bonds defined for protein. 564 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3650 1.03 - 1.23: 66 1.23 - 1.43: 1428 1.43 - 1.62: 2212 1.62 - 1.82: 25 Bond restraints: 7381 Sorted by residual: bond pdb=" C ASP A 196 " pdb=" N PRO A 197 " ideal model delta sigma weight residual 1.334 1.345 -0.011 8.40e-03 1.42e+04 1.76e+00 bond pdb=" CB LYS A 460 " pdb=" CG LYS A 460 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.59e-01 bond pdb=" CA THR A 393 " pdb=" CB THR A 393 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.36e-02 5.41e+03 6.20e-01 bond pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 1.526 1.535 -0.009 1.23e-02 6.61e+03 5.08e-01 bond pdb=" C ASP W 23 " pdb=" N PRO W 24 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.05e-01 ... (remaining 7376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 13107 1.55 - 3.09: 248 3.09 - 4.64: 26 4.64 - 6.19: 3 6.19 - 7.73: 1 Bond angle restraints: 13385 Sorted by residual: angle pdb=" CB MET W 11 " pdb=" CG MET W 11 " pdb=" SD MET W 11 " ideal model delta sigma weight residual 112.70 120.43 -7.73 3.00e+00 1.11e-01 6.65e+00 angle pdb=" C LYS A 436 " pdb=" N VAL A 437 " pdb=" CA VAL A 437 " ideal model delta sigma weight residual 121.97 117.64 4.33 1.80e+00 3.09e-01 5.78e+00 angle pdb=" OG1 THR A 393 " pdb=" CB THR A 393 " pdb=" CG2 THR A 393 " ideal model delta sigma weight residual 109.30 104.65 4.65 2.00e+00 2.50e-01 5.42e+00 angle pdb=" CG MET W 11 " pdb=" SD MET W 11 " pdb=" CE MET W 11 " ideal model delta sigma weight residual 100.90 105.55 -4.65 2.20e+00 2.07e-01 4.46e+00 angle pdb=" CB LYS A 460 " pdb=" CG LYS A 460 " pdb=" CD LYS A 460 " ideal model delta sigma weight residual 111.30 115.52 -4.22 2.30e+00 1.89e-01 3.37e+00 ... (remaining 13380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 2995 16.76 - 33.52: 319 33.52 - 50.27: 104 50.27 - 67.03: 27 67.03 - 83.79: 10 Dihedral angle restraints: 3455 sinusoidal: 1906 harmonic: 1549 Sorted by residual: dihedral pdb=" CA VAL A 435 " pdb=" C VAL A 435 " pdb=" N LYS A 436 " pdb=" CA LYS A 436 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CG LYS A 380 " pdb=" CD LYS A 380 " pdb=" CE LYS A 380 " pdb=" NZ LYS A 380 " ideal model delta sinusoidal sigma weight residual -180.00 -122.66 -57.34 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CB LYS A 460 " pdb=" CG LYS A 460 " pdb=" CD LYS A 460 " pdb=" CE LYS A 460 " ideal model delta sinusoidal sigma weight residual 60.00 116.45 -56.45 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 3452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 368 0.027 - 0.054: 144 0.054 - 0.080: 59 0.080 - 0.107: 24 0.107 - 0.134: 2 Chirality restraints: 597 Sorted by residual: chirality pdb=" CA ILE W 26 " pdb=" N ILE W 26 " pdb=" C ILE W 26 " pdb=" CB ILE W 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA PRO A 308 " pdb=" N PRO A 308 " pdb=" C PRO A 308 " pdb=" CB PRO A 308 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.92e-01 chirality pdb=" CA PRO A 364 " pdb=" N PRO A 364 " pdb=" C PRO A 364 " pdb=" CB PRO A 364 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.63e-01 ... (remaining 594 not shown) Planarity restraints: 1129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 18 " 0.176 9.50e-02 1.11e+02 5.89e-02 4.04e+00 pdb=" NE ARG A 18 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 18 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 18 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 18 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 18 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG A 18 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 18 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 18 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 439 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO A 440 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 307 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 308 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " -0.019 5.00e-02 4.00e+02 ... (remaining 1126 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 727 2.23 - 2.82: 16577 2.82 - 3.41: 21512 3.41 - 4.01: 29235 4.01 - 4.60: 43707 Nonbonded interactions: 111758 Sorted by model distance: nonbonded pdb=" HH TYR A 166 " pdb=" O GLY A 170 " model vdw 1.637 2.450 nonbonded pdb=" H GLY A 48 " pdb=" O HOH A1907 " model vdw 1.706 2.450 nonbonded pdb=" HZ1 LYS A 380 " pdb=" O SER W 29 " model vdw 1.727 2.450 nonbonded pdb=" HH TYR W 21 " pdb=" O HOH W1001 " model vdw 1.734 2.450 nonbonded pdb=" O ALA A 181 " pdb="HD22 ASN A 218 " model vdw 1.747 2.450 ... (remaining 111753 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=0.29 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 : 0.003 0.024 3726 Z= 0.201 Angle : 0.568 7.734 5061 Z= 0.295 Chirality : 0.036 0.134 597 Planarity : 0.005 0.077 668 Dihedral : 17.468 83.789 1365 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.52 % Allowed : 16.80 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.39), residues: 479 helix: 1.75 (0.29), residues: 319 sheet: None (None), residues: 0 loop : 0.03 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 350 PHE 0.009 0.001 PHE A 234 TYR 0.013 0.002 TYR A 455 ARG 0.008 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.528 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 2.7756 time to fit residues: 191.5956 Evaluate side-chains 66 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111684 restraints weight = 10605.982| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.22 r_work: 0.3066 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3726 Z= 0.157 Angle : 0.487 4.949 5061 Z= 0.254 Chirality : 0.036 0.129 597 Planarity : 0.004 0.040 668 Dihedral : 4.447 37.760 511 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.29 % Allowed : 15.25 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.39), residues: 479 helix: 2.11 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.10 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.008 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.005 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.551 Fit side-chains REVERT: A 311 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8841 (mtt) outliers start: 5 outliers final: 1 residues processed: 75 average time/residue: 2.7121 time to fit residues: 209.4305 Evaluate side-chains 71 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113128 restraints weight = 10634.593| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.21 r_work: 0.3079 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.147 Angle : 0.466 4.353 5061 Z= 0.242 Chirality : 0.035 0.129 597 Planarity : 0.004 0.045 668 Dihedral : 4.251 33.747 511 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.52 % Allowed : 15.76 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.39), residues: 479 helix: 2.27 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.16 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.008 0.001 PHE A 234 TYR 0.009 0.002 TYR A 455 ARG 0.006 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7756 (t70) cc_final: 0.7272 (t70) REVERT: A 311 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8833 (mtt) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 2.5670 time to fit residues: 190.5802 Evaluate side-chains 72 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.109771 restraints weight = 10652.949| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.23 r_work: 0.3030 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3726 Z= 0.241 Angle : 0.518 4.454 5061 Z= 0.276 Chirality : 0.038 0.129 597 Planarity : 0.004 0.051 668 Dihedral : 4.308 25.315 509 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.55 % Allowed : 15.25 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.39), residues: 479 helix: 2.03 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.04 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 343 PHE 0.011 0.002 PHE A 234 TYR 0.012 0.003 TYR W 21 ARG 0.004 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.610 Fit side-chains REVERT: A 91 ASP cc_start: 0.8150 (m-30) cc_final: 0.7849 (m-30) REVERT: A 196 ASP cc_start: 0.7775 (t70) cc_final: 0.7285 (t70) REVERT: W 11 MET cc_start: 0.8039 (tpp) cc_final: 0.7680 (tpt) outliers start: 6 outliers final: 2 residues processed: 74 average time/residue: 2.7085 time to fit residues: 206.5954 Evaluate side-chains 72 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 28 optimal weight: 0.0370 chunk 46 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113728 restraints weight = 10690.161| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.22 r_work: 0.3098 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.129 Angle : 0.453 4.369 5061 Z= 0.235 Chirality : 0.035 0.128 597 Planarity : 0.004 0.036 668 Dihedral : 3.897 24.178 509 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.26 % Allowed : 16.80 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.39), residues: 479 helix: 2.36 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.19 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.006 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.004 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.599 Fit side-chains REVERT: A 91 ASP cc_start: 0.8117 (m-30) cc_final: 0.7825 (m-30) REVERT: A 137 GLN cc_start: 0.8355 (pt0) cc_final: 0.8106 (pt0) REVERT: A 196 ASP cc_start: 0.7693 (t70) cc_final: 0.7229 (t70) REVERT: A 311 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8826 (mtt) REVERT: W 11 MET cc_start: 0.7974 (tpp) cc_final: 0.7642 (tpt) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 2.6195 time to fit residues: 197.2008 Evaluate side-chains 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115355 restraints weight = 10680.680| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.21 r_work: 0.3102 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3726 Z= 0.138 Angle : 0.453 4.299 5061 Z= 0.236 Chirality : 0.035 0.128 597 Planarity : 0.004 0.058 668 Dihedral : 3.833 23.660 509 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.52 % Allowed : 16.54 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.40), residues: 479 helix: 2.42 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.26 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 350 PHE 0.007 0.001 PHE A 234 TYR 0.009 0.002 TYR A 455 ARG 0.007 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.535 Fit side-chains REVERT: A 91 ASP cc_start: 0.8122 (m-30) cc_final: 0.7843 (m-30) REVERT: A 137 GLN cc_start: 0.8384 (pt0) cc_final: 0.8105 (pt0) REVERT: A 196 ASP cc_start: 0.7698 (t70) cc_final: 0.7212 (t70) REVERT: A 311 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8828 (mtt) REVERT: A 455 TYR cc_start: 0.7744 (t80) cc_final: 0.7452 (t80) REVERT: W 11 MET cc_start: 0.7983 (tpp) cc_final: 0.7649 (tpt) outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 2.6110 time to fit residues: 193.8706 Evaluate side-chains 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.109909 restraints weight = 10619.136| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.22 r_work: 0.3043 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3726 Z= 0.239 Angle : 0.516 4.464 5061 Z= 0.274 Chirality : 0.038 0.129 597 Planarity : 0.005 0.061 668 Dihedral : 4.267 24.820 509 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.03 % Allowed : 15.76 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.39), residues: 479 helix: 2.13 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.08 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 343 PHE 0.011 0.002 PHE A 234 TYR 0.012 0.003 TYR A 455 ARG 0.005 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.632 Fit side-chains REVERT: A 91 ASP cc_start: 0.8151 (m-30) cc_final: 0.7879 (m-30) REVERT: A 137 GLN cc_start: 0.8400 (pt0) cc_final: 0.8134 (pt0) REVERT: A 196 ASP cc_start: 0.7763 (t70) cc_final: 0.7285 (t70) REVERT: A 363 LYS cc_start: 0.8512 (mtmp) cc_final: 0.8308 (mttm) REVERT: W 11 MET cc_start: 0.8036 (tpp) cc_final: 0.7670 (tpt) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 2.7539 time to fit residues: 206.8275 Evaluate side-chains 73 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.112509 restraints weight = 10707.958| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.23 r_work: 0.3081 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.142 Angle : 0.464 4.383 5061 Z= 0.243 Chirality : 0.035 0.130 597 Planarity : 0.004 0.053 668 Dihedral : 3.996 24.003 509 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.78 % Allowed : 16.28 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.39), residues: 479 helix: 2.32 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.23 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 350 PHE 0.007 0.001 PHE A 234 TYR 0.009 0.002 TYR A 455 ARG 0.006 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.562 Fit side-chains REVERT: A 91 ASP cc_start: 0.8134 (m-30) cc_final: 0.7862 (m-30) REVERT: A 137 GLN cc_start: 0.8367 (pt0) cc_final: 0.8117 (pt0) REVERT: A 196 ASP cc_start: 0.7694 (t70) cc_final: 0.7213 (t70) REVERT: A 311 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8828 (mtt) REVERT: A 363 LYS cc_start: 0.8516 (mtmp) cc_final: 0.8304 (mttm) REVERT: W 11 MET cc_start: 0.8000 (tpp) cc_final: 0.7669 (tpt) outliers start: 3 outliers final: 1 residues processed: 72 average time/residue: 3.1287 time to fit residues: 232.3570 Evaluate side-chains 73 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.131265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113269 restraints weight = 10705.666| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.21 r_work: 0.3053 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3726 Z= 0.192 Angle : 0.488 4.442 5061 Z= 0.258 Chirality : 0.037 0.131 597 Planarity : 0.004 0.051 668 Dihedral : 4.127 24.307 509 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.52 % Allowed : 16.54 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.39), residues: 479 helix: 2.22 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.17 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 383 PHE 0.010 0.001 PHE A 234 TYR 0.011 0.002 TYR A 455 ARG 0.004 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.534 Fit side-chains REVERT: A 91 ASP cc_start: 0.8132 (m-30) cc_final: 0.7865 (m-30) REVERT: A 137 GLN cc_start: 0.8380 (pt0) cc_final: 0.8128 (pt0) REVERT: A 196 ASP cc_start: 0.7723 (t70) cc_final: 0.7264 (t70) REVERT: A 311 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8843 (mtt) REVERT: A 363 LYS cc_start: 0.8525 (mtmp) cc_final: 0.8320 (mttm) REVERT: W 11 MET cc_start: 0.8051 (tpp) cc_final: 0.7717 (tpt) outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 2.9931 time to fit residues: 216.0741 Evaluate side-chains 72 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113767 restraints weight = 10788.979| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.24 r_work: 0.3089 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3726 Z= 0.132 Angle : 0.456 4.354 5061 Z= 0.238 Chirality : 0.035 0.130 597 Planarity : 0.004 0.049 668 Dihedral : 3.885 23.555 509 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.78 % Allowed : 16.28 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.39), residues: 479 helix: 2.40 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.30 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 350 PHE 0.006 0.001 PHE A 234 TYR 0.009 0.002 TYR A 455 ARG 0.005 0.000 ARG A 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 168 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.935 Fit side-chains REVERT: A 91 ASP cc_start: 0.8120 (m-30) cc_final: 0.7856 (m-30) REVERT: A 137 GLN cc_start: 0.8364 (pt0) cc_final: 0.8119 (pt0) REVERT: A 196 ASP cc_start: 0.7677 (t70) cc_final: 0.7213 (t70) REVERT: A 311 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8824 (mtt) REVERT: A 363 LYS cc_start: 0.8509 (mtmp) cc_final: 0.8298 (mttm) REVERT: W 11 MET cc_start: 0.8010 (tpp) cc_final: 0.7697 (tpt) outliers start: 3 outliers final: 1 residues processed: 72 average time/residue: 3.1713 time to fit residues: 236.2929 Evaluate side-chains 73 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 0.0570 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.115191 restraints weight = 10615.801| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.21 r_work: 0.3107 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3726 Z= 0.127 Angle : 0.448 4.352 5061 Z= 0.233 Chirality : 0.034 0.130 597 Planarity : 0.004 0.047 668 Dihedral : 3.760 22.793 509 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.78 % Allowed : 16.28 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.40), residues: 479 helix: 2.48 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.34 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.006 0.001 PHE A 234 TYR 0.009 0.001 TYR A 455 ARG 0.005 0.000 ARG A 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9275.12 seconds wall clock time: 160 minutes 31.18 seconds (9631.18 seconds total)