Starting phenix.real_space_refine on Tue Aug 4 21:10:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n5n_48929/08_2026/9n5n_48929.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n5n_48929/08_2026/9n5n_48929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n5n_48929/08_2026/9n5n_48929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n5n_48929/08_2026/9n5n_48929.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n5n_48929/08_2026/9n5n_48929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n5n_48929/08_2026/9n5n_48929.map" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.077 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 52 5.16 5 Na 4 4.78 5 C 4458 2.51 5 N 1044 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6698 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3336 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 428} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' NA': 2, 'AKG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B Time building chain proxies: 2.47, per 1000 atoms: 0.37 Number of scatterers: 6698 At special positions: 0 Unit cell: (83.325, 103.125, 75.075, 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 52 16.00 Na 4 11.00 O 1140 8.00 N 1044 7.00 C 4458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 409.5 milliseconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1652 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 85.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 19 through 39 Processing helix chain 'A' and resid 42 through 62 Processing helix chain 'A' and resid 65 through 80 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.556A pdb=" N PHE A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'A' and resid 150 through 167 Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 174 through 193 removed outlier: 3.743A pdb=" N TYR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.549A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 241 removed outlier: 3.820A pdb=" N PHE A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Proline residue: A 223 - end of helix Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 258 through 277 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.650A pdb=" N GLY A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 355 removed outlier: 4.818A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 377 through 396 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.693A pdb=" N SER A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 434 through 462 removed outlier: 4.149A pdb=" N GLN A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 Processing helix chain 'B' and resid 42 through 62 Processing helix chain 'B' and resid 65 through 80 Proline residue: B 74 - end of helix Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 113 removed outlier: 3.556A pdb=" N PHE B 98 " --> pdb=" O ASN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 130 through 146 Processing helix chain 'B' and resid 150 through 167 Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 174 through 193 removed outlier: 3.743A pdb=" N TYR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.549A pdb=" N ALA B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 241 removed outlier: 3.820A pdb=" N PHE B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) Proline residue: B 223 - end of helix Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 258 through 277 Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 319 through 339 removed outlier: 3.650A pdb=" N GLY B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 355 removed outlier: 4.818A pdb=" N ASP B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N MET B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 373 Processing helix chain 'B' and resid 377 through 396 Proline residue: B 387 - end of helix Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.694A pdb=" N SER B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 429 Processing helix chain 'B' and resid 434 through 462 removed outlier: 4.149A pdb=" N GLN B 462 " --> pdb=" O MET B 458 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1575 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: 0.76 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1098 1.33 - 1.45: 1735 1.45 - 1.57: 3917 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 6848 Sorted by residual: bond pdb=" CA ALA B 195 " pdb=" CB ALA B 195 " ideal model delta sigma weight residual 1.528 1.484 0.045 1.66e-02 3.63e+03 7.29e+00 bond pdb=" CA ALA A 195 " pdb=" CB ALA A 195 " ideal model delta sigma weight residual 1.528 1.484 0.045 1.66e-02 3.63e+03 7.23e+00 bond pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.29e-02 6.01e+03 5.10e+00 bond pdb=" C GLU B 374 " pdb=" O GLU B 374 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.31e-02 5.83e+03 4.88e+00 bond pdb=" C GLU A 374 " pdb=" O GLU A 374 " ideal model delta sigma weight residual 1.236 1.207 0.028 1.31e-02 5.83e+03 4.72e+00 ... (remaining 6843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 8922 1.14 - 2.27: 300 2.27 - 3.41: 69 3.41 - 4.54: 25 4.54 - 5.68: 20 Bond angle restraints: 9336 Sorted by residual: angle pdb=" N VAL B 198 " pdb=" CA VAL B 198 " pdb=" C VAL B 198 " ideal model delta sigma weight residual 112.17 107.83 4.34 9.50e-01 1.11e+00 2.09e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 112.17 107.84 4.33 9.50e-01 1.11e+00 2.08e+01 angle pdb=" O ILE B 194 " pdb=" C ILE B 194 " pdb=" N ALA B 195 " ideal model delta sigma weight residual 122.12 117.26 4.86 1.38e+00 5.25e-01 1.24e+01 angle pdb=" O ILE A 194 " pdb=" C ILE A 194 " pdb=" N ALA A 195 " ideal model delta sigma weight residual 122.12 117.32 4.80 1.38e+00 5.25e-01 1.21e+01 angle pdb=" N ALA A 195 " pdb=" CA ALA A 195 " pdb=" C ALA A 195 " ideal model delta sigma weight residual 111.82 115.67 -3.85 1.16e+00 7.43e-01 1.10e+01 ... (remaining 9331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 3730 17.61 - 35.21: 208 35.21 - 52.82: 8 52.82 - 70.42: 6 70.42 - 88.03: 6 Dihedral angle restraints: 3958 sinusoidal: 1410 harmonic: 2548 Sorted by residual: dihedral pdb=" CA ASN B 245 " pdb=" CB ASN B 245 " pdb=" CG ASN B 245 " pdb=" OD1 ASN B 245 " ideal model delta sinusoidal sigma weight residual -90.00 -154.40 64.40 2 2.00e+01 2.50e-03 9.76e+00 dihedral pdb=" CA ASN A 245 " pdb=" CB ASN A 245 " pdb=" CG ASN A 245 " pdb=" OD1 ASN A 245 " ideal model delta sinusoidal sigma weight residual -90.00 -154.36 64.36 2 2.00e+01 2.50e-03 9.75e+00 dihedral pdb=" CA LEU A 402 " pdb=" CB LEU A 402 " pdb=" CG LEU A 402 " pdb=" CD1 LEU A 402 " ideal model delta sinusoidal sigma weight residual 180.00 143.76 36.24 3 1.50e+01 4.44e-03 6.26e+00 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 865 0.041 - 0.081: 230 0.081 - 0.122: 49 0.122 - 0.162: 10 0.162 - 0.203: 2 Chirality restraints: 1156 Sorted by residual: chirality pdb=" CA VAL B 198 " pdb=" N VAL B 198 " pdb=" C VAL B 198 " pdb=" CB VAL B 198 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL A 198 " pdb=" N VAL A 198 " pdb=" C VAL A 198 " pdb=" CB VAL A 198 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL B 198 " pdb=" CA VAL B 198 " pdb=" CG1 VAL B 198 " pdb=" CG2 VAL B 198 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 1153 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 421 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO B 422 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 422 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 422 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 421 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 422 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 200 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 201 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.021 5.00e-02 4.00e+02 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 198 2.72 - 3.27: 7141 3.27 - 3.81: 11591 3.81 - 4.36: 13660 4.36 - 4.90: 23897 Nonbonded interactions: 56487 Sorted by model distance: nonbonded pdb=" O ASN B 245 " pdb=" ND2 ASN B 245 " model vdw 2.179 3.120 nonbonded pdb=" O ASN A 245 " pdb=" ND2 ASN A 245 " model vdw 2.179 3.120 nonbonded pdb=" O VAL B 169 " pdb=" OH TYR B 178 " model vdw 2.227 3.040 nonbonded pdb=" O VAL A 169 " pdb=" OH TYR A 178 " model vdw 2.228 3.040 nonbonded pdb=" O SER A 150 " pdb=" OG1 THR A 154 " model vdw 2.288 3.040 ... (remaining 56482 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 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 0.045 6848 Z= 0.180 Angle : 0.587 5.679 9336 Z= 0.351 Chirality : 0.039 0.203 1156 Planarity : 0.004 0.039 1134 Dihedral : 11.230 88.026 2306 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.28), residues: 884 helix: 1.34 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.91 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.012 0.001 TYR B 178 PHE 0.010 0.001 PHE B 100 TRP 0.013 0.001 TRP A 217 HIS 0.003 0.000 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.18 ( 6848) covalent geometry : angle 0.58724 / 0.35 ( 9336) hydrogen bonds : bond 0.10571 / 7.04 ( 525) hydrogen bonds : angle 5.00061 / 3.66 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 133 average time/residue: 0.4520 time to fit residues: 63.1978 Evaluate side-chains 108 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 245 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN A 347 ASN B 94 ASN B 338 GLN B 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.079097 restraints weight = 7552.812| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.76 r_work: 0.2762 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6848 Z= 0.160 Angle : 0.538 5.668 9336 Z= 0.285 Chirality : 0.037 0.121 1156 Planarity : 0.005 0.071 1134 Dihedral : 5.869 88.967 920 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.27 % Allowed : 5.97 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.28), residues: 884 helix: 2.00 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.58 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.009 0.001 TYR A 178 PHE 0.010 0.002 PHE A 371 TRP 0.011 0.002 TRP B 311 HIS 0.003 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 6848) covalent geometry : angle 0.53830 / 0.28 ( 9336) hydrogen bonds : bond 0.04981 / 3.37 ( 525) hydrogen bonds : angle 4.05993 / 2.97 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.155 Fit side-chains REVERT: A 313 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7615 (mp0) REVERT: B 259 LYS cc_start: 0.7143 (tmmt) cc_final: 0.6939 (tmmt) REVERT: B 313 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7580 (mp0) outliers start: 16 outliers final: 4 residues processed: 128 average time/residue: 0.5117 time to fit residues: 68.5424 Evaluate side-chains 116 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 459 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 23 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 ASN A 338 GLN A 347 ASN B 245 ASN B 338 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.081229 restraints weight = 7648.215| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.75 r_work: 0.2792 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6848 Z= 0.105 Angle : 0.455 5.376 9336 Z= 0.240 Chirality : 0.035 0.108 1156 Planarity : 0.004 0.045 1134 Dihedral : 5.411 87.131 916 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.42 % Allowed : 10.09 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.29), residues: 884 helix: 2.31 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.40 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.006 0.001 TYR B 36 PHE 0.009 0.001 PHE B 277 TRP 0.013 0.001 TRP A 311 HIS 0.001 0.000 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 6848) covalent geometry : angle 0.45463 / 0.24 ( 9336) hydrogen bonds : bond 0.03964 / 2.71 ( 525) hydrogen bonds : angle 3.86288 / 2.83 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.239 Fit side-chains REVERT: A 157 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8329 (tmt) REVERT: A 313 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7529 (mt-10) REVERT: B 313 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7433 (mt-10) outliers start: 10 outliers final: 3 residues processed: 116 average time/residue: 0.4947 time to fit residues: 60.2049 Evaluate side-chains 115 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 245 ASN A 334 ASN A 338 GLN A 347 ASN B 91 ASN B 245 ASN B 334 ASN B 338 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.075774 restraints weight = 7700.422| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.77 r_work: 0.2698 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6848 Z= 0.156 Angle : 0.507 5.586 9336 Z= 0.270 Chirality : 0.037 0.108 1156 Planarity : 0.004 0.045 1134 Dihedral : 5.584 86.820 916 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.56 % Allowed : 9.09 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.28), residues: 884 helix: 2.29 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.38 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.006 0.001 TYR B 36 PHE 0.011 0.001 PHE B 136 TRP 0.017 0.002 TRP A 311 HIS 0.003 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 6848) covalent geometry : angle 0.50692 / 0.27 ( 9336) hydrogen bonds : bond 0.04812 / 3.29 ( 525) hydrogen bonds : angle 3.97884 / 2.91 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.201 Fit side-chains REVERT: A 313 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7673 (mp0) REVERT: A 354 SER cc_start: 0.6768 (OUTLIER) cc_final: 0.6476 (p) REVERT: B 313 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7534 (mp0) REVERT: B 347 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8058 (m-40) outliers start: 18 outliers final: 7 residues processed: 125 average time/residue: 0.4845 time to fit residues: 63.6299 Evaluate side-chains 128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 ASN A 338 GLN A 347 ASN B 245 ASN B 338 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.075585 restraints weight = 7712.277| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.76 r_work: 0.2695 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6848 Z= 0.144 Angle : 0.495 5.499 9336 Z= 0.263 Chirality : 0.036 0.107 1156 Planarity : 0.004 0.046 1134 Dihedral : 5.519 84.997 916 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.27 % Allowed : 10.65 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.28), residues: 884 helix: 2.34 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.23 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.005 0.001 TYR B 36 PHE 0.009 0.001 PHE B 277 TRP 0.018 0.002 TRP A 311 HIS 0.003 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 6848) covalent geometry : angle 0.49515 / 0.26 ( 9336) hydrogen bonds : bond 0.04595 / 3.14 ( 525) hydrogen bonds : angle 3.96459 / 2.90 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.154 Fit side-chains REVERT: A 313 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7640 (mp0) REVERT: A 354 SER cc_start: 0.6911 (OUTLIER) cc_final: 0.6635 (p) REVERT: B 313 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7515 (mp0) REVERT: B 347 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8089 (m110) REVERT: B 354 SER cc_start: 0.6835 (OUTLIER) cc_final: 0.6543 (p) outliers start: 16 outliers final: 6 residues processed: 123 average time/residue: 0.4888 time to fit residues: 63.0518 Evaluate side-chains 125 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 29 optimal weight: 0.0060 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 ASN A 338 GLN A 347 ASN B 245 ASN B 338 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.078182 restraints weight = 7718.452| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.74 r_work: 0.2744 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6848 Z= 0.107 Angle : 0.459 5.470 9336 Z= 0.241 Chirality : 0.035 0.107 1156 Planarity : 0.004 0.046 1134 Dihedral : 5.235 82.190 916 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.56 % Allowed : 11.22 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.28), residues: 884 helix: 2.48 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.20 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 175 TYR 0.006 0.001 TYR A 178 PHE 0.009 0.001 PHE A 277 TRP 0.016 0.001 TRP B 311 HIS 0.001 0.000 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 6848) covalent geometry : angle 0.45887 / 0.24 ( 9336) hydrogen bonds : bond 0.03992 / 2.73 ( 525) hydrogen bonds : angle 3.84466 / 2.82 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.197 Fit side-chains REVERT: A 313 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7519 (mt-10) REVERT: A 354 SER cc_start: 0.6890 (OUTLIER) cc_final: 0.6622 (p) REVERT: B 313 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7426 (mp0) REVERT: B 347 ASN cc_start: 0.8392 (m110) cc_final: 0.8061 (m110) REVERT: B 354 SER cc_start: 0.6784 (OUTLIER) cc_final: 0.6500 (p) outliers start: 18 outliers final: 7 residues processed: 126 average time/residue: 0.4825 time to fit residues: 63.9204 Evaluate side-chains 128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 435 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 0.0870 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 ASN A 338 GLN A 347 ASN B 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.079304 restraints weight = 7655.421| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.72 r_work: 0.2761 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6848 Z= 0.104 Angle : 0.452 5.388 9336 Z= 0.237 Chirality : 0.034 0.108 1156 Planarity : 0.004 0.044 1134 Dihedral : 5.101 80.778 916 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.99 % Allowed : 11.79 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.29), residues: 884 helix: 2.62 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.21 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.005 0.001 TYR A 178 PHE 0.008 0.001 PHE B 277 TRP 0.016 0.001 TRP B 311 HIS 0.002 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 6848) covalent geometry : angle 0.45205 / 0.24 ( 9336) hydrogen bonds : bond 0.03844 / 2.63 ( 525) hydrogen bonds : angle 3.78415 / 2.77 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.216 Fit side-chains REVERT: A 313 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7483 (mt-10) REVERT: A 354 SER cc_start: 0.7041 (OUTLIER) cc_final: 0.6798 (p) REVERT: A 437 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7905 (pt0) REVERT: B 313 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7405 (mp0) REVERT: B 347 ASN cc_start: 0.8387 (m110) cc_final: 0.8068 (m110) REVERT: B 354 SER cc_start: 0.6817 (OUTLIER) cc_final: 0.6535 (p) REVERT: B 437 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7910 (pt0) outliers start: 14 outliers final: 4 residues processed: 120 average time/residue: 0.4984 time to fit residues: 62.6674 Evaluate side-chains 121 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 87 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 50 optimal weight: 0.0270 chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 ASN A 338 GLN A 347 ASN B 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.078315 restraints weight = 7663.376| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.74 r_work: 0.2743 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6848 Z= 0.110 Angle : 0.457 5.439 9336 Z= 0.240 Chirality : 0.035 0.107 1156 Planarity : 0.004 0.043 1134 Dihedral : 5.124 81.021 916 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.28 % Allowed : 12.50 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.28), residues: 884 helix: 2.64 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.23 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.006 0.001 TYR A 178 PHE 0.009 0.001 PHE B 277 TRP 0.015 0.001 TRP A 311 HIS 0.002 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 6848) covalent geometry : angle 0.45734 / 0.24 ( 9336) hydrogen bonds : bond 0.04002 / 2.74 ( 525) hydrogen bonds : angle 3.80189 / 2.79 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.174 Fit side-chains REVERT: A 313 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7496 (mt-10) REVERT: A 354 SER cc_start: 0.7224 (OUTLIER) cc_final: 0.6993 (p) REVERT: A 437 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7913 (pt0) REVERT: B 313 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7424 (mp0) REVERT: B 347 ASN cc_start: 0.8398 (m110) cc_final: 0.8079 (m110) REVERT: B 354 SER cc_start: 0.6867 (OUTLIER) cc_final: 0.6598 (p) REVERT: B 437 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7899 (pt0) outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 0.4891 time to fit residues: 61.6682 Evaluate side-chains 124 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN A 347 ASN B 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.077421 restraints weight = 7710.092| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.74 r_work: 0.2729 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6848 Z= 0.118 Angle : 0.466 5.449 9336 Z= 0.245 Chirality : 0.035 0.106 1156 Planarity : 0.004 0.043 1134 Dihedral : 5.166 81.001 916 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.85 % Allowed : 12.07 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.28), residues: 884 helix: 2.60 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.19 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.004 0.001 TYR A 178 PHE 0.009 0.001 PHE A 277 TRP 0.016 0.001 TRP B 311 HIS 0.003 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6848) covalent geometry : angle 0.46558 / 0.24 ( 9336) hydrogen bonds : bond 0.04137 / 2.83 ( 525) hydrogen bonds : angle 3.83382 / 2.81 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.197 Fit side-chains REVERT: A 313 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7585 (mp0) REVERT: A 354 SER cc_start: 0.7357 (OUTLIER) cc_final: 0.7135 (p) REVERT: B 313 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7423 (mp0) REVERT: B 347 ASN cc_start: 0.8394 (m110) cc_final: 0.8076 (m110) REVERT: B 354 SER cc_start: 0.7074 (OUTLIER) cc_final: 0.6850 (p) REVERT: B 421 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7103 (p) REVERT: B 437 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7880 (pt0) outliers start: 13 outliers final: 5 residues processed: 119 average time/residue: 0.4877 time to fit residues: 60.9421 Evaluate side-chains 123 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 0.0020 chunk 85 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN A 347 ASN B 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.079341 restraints weight = 7643.396| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.73 r_work: 0.2762 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6848 Z= 0.102 Angle : 0.452 5.386 9336 Z= 0.236 Chirality : 0.035 0.108 1156 Planarity : 0.004 0.043 1134 Dihedral : 5.008 79.069 916 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.14 % Allowed : 12.78 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.29), residues: 884 helix: 2.66 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.30 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 175 TYR 0.005 0.001 TYR A 178 PHE 0.008 0.001 PHE B 277 TRP 0.015 0.001 TRP A 311 HIS 0.002 0.000 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 6848) covalent geometry : angle 0.45240 / 0.24 ( 9336) hydrogen bonds : bond 0.03789 / 2.59 ( 525) hydrogen bonds : angle 3.76577 / 2.76 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.189 Fit side-chains REVERT: A 313 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7495 (mt-10) REVERT: A 437 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7912 (pt0) REVERT: B 313 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7419 (mp0) REVERT: B 347 ASN cc_start: 0.8392 (m110) cc_final: 0.8094 (m110) REVERT: B 354 SER cc_start: 0.7073 (OUTLIER) cc_final: 0.6857 (p) REVERT: B 437 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7886 (pt0) outliers start: 8 outliers final: 5 residues processed: 119 average time/residue: 0.4940 time to fit residues: 61.7511 Evaluate side-chains 122 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN A 347 ASN B 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.075531 restraints weight = 7643.918| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.75 r_work: 0.2697 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6848 Z= 0.146 Angle : 0.496 5.571 9336 Z= 0.261 Chirality : 0.036 0.106 1156 Planarity : 0.004 0.043 1134 Dihedral : 5.289 81.829 916 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.14 % Allowed : 13.07 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.28), residues: 884 helix: 2.56 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.004 0.001 TYR B 36 PHE 0.009 0.001 PHE B 136 TRP 0.016 0.002 TRP B 311 HIS 0.003 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 6848) covalent geometry : angle 0.49610 / 0.26 ( 9336) hydrogen bonds : bond 0.04525 / 3.09 ( 525) hydrogen bonds : angle 3.90618 / 2.86 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2205.10 seconds wall clock time: 38 minutes 3.28 seconds (2283.28 seconds total)