Starting phenix.real_space_refine on Wed Feb 12 03:49:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzu_26918/02_2025/7uzu_26918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzu_26918/02_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_26918/02_2025/7uzu_26918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzu_26918/02_2025/7uzu_26918.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzu_26918/02_2025/7uzu_26918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzu_26918/02_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-5592/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: 4.39, per 1000 atoms: 0.59 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: 1.86 Conformation dependent library (CDL) restraints added in 610.6 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: 2.64 Time building geometry restraints manager: 2.21 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: 1.530 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: 0.160 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- 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 : 0.623 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 3.0167 time to fit residues: 208.0625 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 : 0.590 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.130140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112037 restraints weight = 10614.316| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.22 r_work: 0.3072 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0568 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= 0.148 Angle : 0.482 4.952 5061 Z= 0.251 Chirality : 0.035 0.129 597 Planarity : 0.004 0.039 668 Dihedral : 4.402 37.450 511 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 : 0.78 % Allowed : 15.76 % 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: 2.19 (0.39), residues: 479 helix: 2.13 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.12 (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 0.004 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 76 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.598 Fit side-chains REVERT: A 311 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8838 (mtt) outliers start: 3 outliers final: 0 residues processed: 74 average time/residue: 2.7563 time to fit residues: 210.0745 Evaluate side-chains 71 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.129524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111339 restraints weight = 10623.844| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.22 r_work: 0.3064 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0652 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= 0.167 Angle : 0.479 4.389 5061 Z= 0.250 Chirality : 0.036 0.129 597 Planarity : 0.004 0.048 668 Dihedral : 4.071 24.629 509 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.78 % Allowed : 15.76 % 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: 2.26 (0.39), residues: 479 helix: 2.19 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.13 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 162 PHE 0.009 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.005 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 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 91 ASP cc_start: 0.8131 (m-30) cc_final: 0.7813 (m-30) REVERT: A 196 ASP cc_start: 0.7779 (t70) cc_final: 0.7285 (t70) REVERT: A 311 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8845 (mtt) outliers start: 3 outliers final: 0 residues processed: 73 average time/residue: 2.7312 time to fit residues: 205.6022 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 : 0.580 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.130946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112887 restraints weight = 10682.941| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.22 r_work: 0.3071 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0764 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= 0.151 Angle : 0.467 4.397 5061 Z= 0.244 Chirality : 0.035 0.129 597 Planarity : 0.004 0.048 668 Dihedral : 3.990 24.348 509 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.03 % Allowed : 15.50 % 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: 2.37 (0.39), residues: 479 helix: 2.28 (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 0.002 0.001 HIS A 162 PHE 0.008 0.001 PHE A 234 TYR 0.009 0.002 TYR A 455 ARG 0.005 0.000 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 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 91 ASP cc_start: 0.8127 (m-30) cc_final: 0.7838 (m-30) REVERT: A 137 GLN cc_start: 0.8367 (pt0) cc_final: 0.8112 (pt0) REVERT: A 196 ASP cc_start: 0.7726 (t70) cc_final: 0.7259 (t70) REVERT: A 311 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8835 (mtt) REVERT: W 11 MET cc_start: 0.8017 (tpp) cc_final: 0.7668 (tpt) outliers start: 4 outliers final: 0 residues processed: 73 average time/residue: 2.7565 time to fit residues: 207.7327 Evaluate side-chains 73 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.128541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.110210 restraints weight = 10737.900| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.23 r_work: 0.3035 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 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 = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.0734 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= 0.214 Angle : 0.500 4.443 5061 Z= 0.265 Chirality : 0.037 0.128 597 Planarity : 0.004 0.054 668 Dihedral : 4.203 24.935 509 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.03 % Allowed : 15.50 % 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: 2.19 (0.39), residues: 479 helix: 2.14 (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 0.010 0.001 PHE A 234 TYR 0.011 0.002 TYR W 21 ARG 0.005 0.001 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: 4 poor density : 70 time to evaluate : 0.563 Fit side-chains REVERT: A 91 ASP cc_start: 0.8137 (m-30) cc_final: 0.7864 (m-30) REVERT: A 137 GLN cc_start: 0.8380 (pt0) cc_final: 0.8113 (pt0) REVERT: A 196 ASP cc_start: 0.7754 (t70) cc_final: 0.7283 (t70) REVERT: W 11 MET cc_start: 0.8030 (tpp) cc_final: 0.7668 (tpt) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 2.8023 time to fit residues: 211.0443 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 : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 421 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.132352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114375 restraints weight = 10674.823| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.22 r_work: 0.3089 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 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 = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0881 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 : 0.457 4.369 5061 Z= 0.237 Chirality : 0.035 0.130 597 Planarity : 0.004 0.056 668 Dihedral : 3.898 24.079 509 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: 2.51 (0.39), residues: 479 helix: 2.38 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.22 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.007 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.006 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 75 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.544 Fit side-chains REVERT: A 91 ASP cc_start: 0.8116 (m-30) cc_final: 0.7845 (m-30) REVERT: A 128 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7982 (tttp) REVERT: A 137 GLN cc_start: 0.8365 (pt0) cc_final: 0.8117 (pt0) REVERT: A 196 ASP cc_start: 0.7700 (t70) cc_final: 0.7233 (t70) REVERT: A 311 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8826 (mtt) REVERT: W 11 MET cc_start: 0.7990 (tpp) cc_final: 0.7657 (tpt) outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 2.8822 time to fit residues: 216.5398 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 : 0.591 ------------------------------------------------------------------------------- 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: 5.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.131199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.113250 restraints weight = 10628.911| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.20 r_work: 0.3062 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3726 Z= 0.178 Angle : 0.484 4.414 5061 Z= 0.253 Chirality : 0.036 0.131 597 Planarity : 0.004 0.060 668 Dihedral : 4.041 24.371 509 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.78 % Allowed : 16.02 % 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: 2.42 (0.39), residues: 479 helix: 2.30 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.21 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 383 PHE 0.009 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.006 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 73 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.603 Fit side-chains REVERT: A 91 ASP cc_start: 0.8124 (m-30) cc_final: 0.7861 (m-30) REVERT: A 137 GLN cc_start: 0.8391 (pt0) cc_final: 0.8139 (pt0) REVERT: A 196 ASP cc_start: 0.7747 (t70) cc_final: 0.7273 (t70) REVERT: A 311 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8840 (mtt) REVERT: W 11 MET cc_start: 0.8017 (tpp) cc_final: 0.7677 (tpt) outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 2.7754 time to fit residues: 205.7741 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 : 0.553 ------------------------------------------------------------------------------- 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: 6.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.131508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113456 restraints weight = 10709.731| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.22 r_work: 0.3069 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0863 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= 0.164 Angle : 0.480 4.402 5061 Z= 0.250 Chirality : 0.036 0.130 597 Planarity : 0.004 0.061 668 Dihedral : 4.016 24.254 509 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.03 % Allowed : 16.28 % 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: 2.44 (0.39), residues: 479 helix: 2.31 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.24 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 343 PHE 0.009 0.001 PHE A 234 TYR 0.010 0.002 TYR A 455 ARG 0.007 0.001 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 72 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.556 Fit side-chains REVERT: A 91 ASP cc_start: 0.8121 (m-30) cc_final: 0.7858 (m-30) REVERT: A 137 GLN cc_start: 0.8394 (pt0) cc_final: 0.8141 (pt0) REVERT: A 196 ASP cc_start: 0.7718 (t70) cc_final: 0.7240 (t70) REVERT: A 311 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8840 (mtt) REVERT: W 11 MET cc_start: 0.8018 (tpp) cc_final: 0.7686 (tpt) outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 2.7736 time to fit residues: 202.9226 Evaluate side-chains 72 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 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: 0.8980 chunk 12 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.131466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113281 restraints weight = 10702.140| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.23 r_work: 0.3074 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 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 = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0893 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= 0.148 Angle : 0.470 4.390 5061 Z= 0.244 Chirality : 0.035 0.130 597 Planarity : 0.004 0.063 668 Dihedral : 3.933 23.897 509 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.55 % Allowed : 15.76 % 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: 2.52 (0.39), residues: 479 helix: 2.37 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.29 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 350 PHE 0.008 0.001 PHE A 234 TYR 0.009 0.002 TYR A 455 ARG 0.007 0.000 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 76 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.665 Fit side-chains REVERT: A 91 ASP cc_start: 0.8121 (m-30) cc_final: 0.7861 (m-30) REVERT: A 137 GLN cc_start: 0.8385 (pt0) cc_final: 0.8137 (pt0) REVERT: A 196 ASP cc_start: 0.7704 (t70) cc_final: 0.7231 (t70) REVERT: A 311 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8831 (mtt) REVERT: W 11 MET cc_start: 0.8006 (tpp) cc_final: 0.7685 (tpt) outliers start: 6 outliers final: 2 residues processed: 74 average time/residue: 2.7243 time to fit residues: 207.9324 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 : 0.700 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.133366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115312 restraints weight = 10789.670| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.22 r_work: 0.3101 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 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 = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1026 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= 0.130 Angle : 0.454 4.370 5061 Z= 0.234 Chirality : 0.034 0.130 597 Planarity : 0.004 0.060 668 Dihedral : 3.746 23.058 509 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 : 0.52 % Allowed : 17.05 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.69 (0.40), residues: 479 helix: 2.49 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.36 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 83 PHE 0.005 0.001 PHE A 234 TYR 0.008 0.001 TYR A 455 ARG 0.007 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: 2 poor density : 72 time to evaluate : 0.562 Fit side-chains REVERT: A 91 ASP cc_start: 0.8112 (m-30) cc_final: 0.7859 (m-30) REVERT: A 137 GLN cc_start: 0.8379 (pt0) cc_final: 0.8113 (pt0) REVERT: A 196 ASP cc_start: 0.7662 (t70) cc_final: 0.7196 (t70) REVERT: A 311 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8817 (mtt) outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 2.6295 time to fit residues: 195.1816 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 : 0.569 ------------------------------------------------------------------------------- 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: 9.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.134105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116216 restraints weight = 10592.964| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.21 r_work: 0.3109 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1012 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= 0.133 Angle : 0.458 4.355 5061 Z= 0.236 Chirality : 0.034 0.130 597 Planarity : 0.004 0.058 668 Dihedral : 3.729 22.643 509 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.78 % Allowed : 16.80 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.71 (0.40), residues: 479 helix: 2.49 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.40 (0.54), 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 0.008 0.002 TYR A 455 ARG 0.007 0.000 ARG A 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8192.70 seconds wall clock time: 144 minutes 27.20 seconds (8667.20 seconds total)