Starting phenix.real_space_refine on Thu Mar 6 09:25:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo3_36454/03_2025/8jo3_36454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo3_36454/03_2025/8jo3_36454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jo3_36454/03_2025/8jo3_36454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo3_36454/03_2025/8jo3_36454.map" model { file = "/net/cci-nas-00/data/ceres_data/8jo3_36454/03_2025/8jo3_36454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo3_36454/03_2025/8jo3_36454.cif" } resolution = 2.66 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= -0.002 sd= 0.151 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 27 5.16 5 C 3619 2.51 5 N 953 2.21 5 O 1111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5715 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2851 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2809 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.75, per 1000 atoms: 0.66 Number of scatterers: 5715 At special positions: 0 Unit cell: (64.17, 79.05, 114.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 27 16.00 P 4 15.00 O 1111 8.00 N 953 7.00 C 3619 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: 1.47 Conformation dependent library (CDL) restraints added in 799.8 milliseconds 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1348 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 61.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 20 through 37 Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.560A pdb=" N PHE A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 72 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 77 through 91 removed outlier: 3.541A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 118 Processing helix chain 'A' and resid 121 through 134 removed outlier: 4.280A pdb=" N PHE A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.806A pdb=" N SER A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 288 through 297 removed outlier: 3.724A pdb=" N VAL A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.537A pdb=" N ALA A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 352 Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.512A pdb=" N SER B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 254 through 262 Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 263 through 264 No H-bonds generated for 'chain 'B' and resid 263 through 264' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 288 through 298 removed outlier: 4.415A pdb=" N LYS B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASP B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.944A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.772A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 193 Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.350A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.603A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 243 320 hydrogen bonds defined for protein. 882 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: 2.24 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1851 1.34 - 1.46: 1006 1.46 - 1.57: 2920 1.57 - 1.69: 6 1.69 - 1.81: 47 Bond restraints: 5830 Sorted by residual: bond pdb=" N ASP B 159 " pdb=" CA ASP B 159 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.56e+00 bond pdb=" N TYR B 145 " pdb=" CA TYR B 145 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.28e+00 bond pdb=" N SER B 157 " pdb=" CA SER B 157 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.27e-02 6.20e+03 4.63e+00 bond pdb=" N GLY B 158 " pdb=" CA GLY B 158 " ideal model delta sigma weight residual 1.449 1.476 -0.027 1.45e-02 4.76e+03 3.51e+00 bond pdb=" N ASP B 156 " pdb=" CA ASP B 156 " ideal model delta sigma weight residual 1.463 1.487 -0.025 1.37e-02 5.33e+03 3.23e+00 ... (remaining 5825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 7791 1.90 - 3.79: 93 3.79 - 5.69: 14 5.69 - 7.58: 0 7.58 - 9.48: 1 Bond angle restraints: 7899 Sorted by residual: angle pdb=" CA ASP B 156 " pdb=" C ASP B 156 " pdb=" O ASP B 156 " ideal model delta sigma weight residual 121.39 118.26 3.13 1.12e+00 7.97e-01 7.82e+00 angle pdb=" CA SER B 157 " pdb=" C SER B 157 " pdb=" O SER B 157 " ideal model delta sigma weight residual 120.54 118.12 2.42 1.04e+00 9.25e-01 5.40e+00 angle pdb=" C GLY A 227 " pdb=" N GLY A 228 " pdb=" CA GLY A 228 " ideal model delta sigma weight residual 120.10 122.24 -2.14 9.50e-01 1.11e+00 5.08e+00 angle pdb=" O TYR B 145 " pdb=" C TYR B 145 " pdb=" N ALA B 146 " ideal model delta sigma weight residual 122.12 124.15 -2.03 1.06e+00 8.90e-01 3.65e+00 angle pdb=" N TYR B 145 " pdb=" CA TYR B 145 " pdb=" C TYR B 145 " ideal model delta sigma weight residual 111.28 109.22 2.06 1.09e+00 8.42e-01 3.56e+00 ... (remaining 7894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 3247 26.44 - 52.88: 272 52.88 - 79.32: 43 79.32 - 105.76: 5 105.76 - 132.20: 1 Dihedral angle restraints: 3568 sinusoidal: 1479 harmonic: 2089 Sorted by residual: dihedral pdb=" C5' AMP A 501 " pdb=" O5' AMP A 501 " pdb=" P AMP A 501 " pdb=" O3P AMP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 167.80 132.20 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CG ARG B 337 " pdb=" CD ARG B 337 " pdb=" NE ARG B 337 " pdb=" CZ ARG B 337 " ideal model delta sinusoidal sigma weight residual 180.00 137.78 42.22 2 1.50e+01 4.44e-03 9.63e+00 ... (remaining 3565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 536 0.031 - 0.062: 237 0.062 - 0.092: 66 0.092 - 0.123: 45 0.123 - 0.154: 1 Chirality restraints: 885 Sorted by residual: chirality pdb=" CB THR A 331 " pdb=" CA THR A 331 " pdb=" OG1 THR A 331 " pdb=" CG2 THR A 331 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CB ILE B 252 " pdb=" CA ILE B 252 " pdb=" CG1 ILE B 252 " pdb=" CG2 ILE B 252 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA VAL B 19 " pdb=" N VAL B 19 " pdb=" C VAL B 19 " pdb=" CB VAL B 19 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 882 not shown) Planarity restraints: 1005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO A 212 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 323 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO B 324 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 324 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 333 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 334 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 334 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 334 " -0.016 5.00e-02 4.00e+02 ... (remaining 1002 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 417 2.74 - 3.28: 5786 3.28 - 3.82: 10492 3.82 - 4.36: 12799 4.36 - 4.90: 21407 Nonbonded interactions: 50901 Sorted by model distance: nonbonded pdb=" OH TYR A 108 " pdb=" O ALA A 315 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLU A 343 " pdb=" OG1 THR B 353 " model vdw 2.204 3.040 nonbonded pdb=" O LEU A 158 " pdb=" N6 AMP A 501 " model vdw 2.251 3.120 nonbonded pdb=" O SER B 35 " pdb=" OG SER B 35 " model vdw 2.273 3.040 nonbonded pdb=" O ILE A 25 " pdb=" OG1 THR A 29 " model vdw 2.275 3.040 ... (remaining 50896 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=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: 1.240 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.220 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 0.036 5830 Z= 0.202 Angle : 0.526 9.477 7899 Z= 0.277 Chirality : 0.041 0.154 885 Planarity : 0.004 0.050 1005 Dihedral : 18.818 132.198 2220 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.56 % Allowed : 23.56 % Favored : 73.88 % 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: 1.75 (0.33), residues: 703 helix: 1.68 (0.27), residues: 375 sheet: 0.01 (0.57), residues: 77 loop : 0.97 (0.45), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 260 PHE 0.014 0.001 PHE A 125 TYR 0.011 0.001 TYR A 42 ARG 0.002 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.677 Fit side-chains REVERT: A 92 THR cc_start: 0.8263 (m) cc_final: 0.8061 (p) REVERT: B 83 ASP cc_start: 0.8103 (m-30) cc_final: 0.7755 (m-30) outliers start: 16 outliers final: 15 residues processed: 108 average time/residue: 1.1693 time to fit residues: 132.3469 Evaluate side-chains 105 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 148 ASN A 272 ASN A 300 HIS A 332 GLN B 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.123071 restraints weight = 5720.531| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.39 r_work: 0.3267 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5830 Z= 0.228 Angle : 0.530 6.618 7899 Z= 0.271 Chirality : 0.042 0.130 885 Planarity : 0.004 0.050 1005 Dihedral : 9.414 125.017 835 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.04 % Allowed : 20.67 % Favored : 76.28 % 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: 1.76 (0.33), residues: 703 helix: 1.62 (0.27), residues: 379 sheet: 0.11 (0.55), residues: 80 loop : 1.06 (0.46), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 277 HIS 0.003 0.001 HIS A 287 PHE 0.015 0.001 PHE A 125 TYR 0.013 0.001 TYR A 42 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.591 Fit side-chains REVERT: A 187 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: B 74 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6666 (pp20) REVERT: B 97 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7067 (mtp180) outliers start: 19 outliers final: 6 residues processed: 106 average time/residue: 1.3023 time to fit residues: 143.8569 Evaluate side-chains 97 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 20 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 300 HIS B 94 ASN B 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.151303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122167 restraints weight = 5682.468| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.39 r_work: 0.3297 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5830 Z= 0.194 Angle : 0.507 6.450 7899 Z= 0.259 Chirality : 0.041 0.130 885 Planarity : 0.004 0.050 1005 Dihedral : 8.198 110.772 815 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.21 % Allowed : 21.47 % Favored : 75.32 % 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: 1.85 (0.33), residues: 703 helix: 1.69 (0.27), residues: 380 sheet: 0.15 (0.54), residues: 80 loop : 1.10 (0.46), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.003 0.001 HIS A 287 PHE 0.013 0.001 PHE A 125 TYR 0.013 0.001 TYR A 42 ARG 0.003 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: B 74 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6648 (pp20) outliers start: 20 outliers final: 8 residues processed: 108 average time/residue: 1.3007 time to fit residues: 146.4465 Evaluate side-chains 98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119607 restraints weight = 5788.681| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.41 r_work: 0.3265 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5830 Z= 0.266 Angle : 0.538 6.630 7899 Z= 0.275 Chirality : 0.043 0.140 885 Planarity : 0.004 0.051 1005 Dihedral : 8.116 98.515 814 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.53 % Allowed : 21.15 % Favored : 75.32 % 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: 1.70 (0.33), residues: 703 helix: 1.49 (0.27), residues: 385 sheet: 0.20 (0.56), residues: 73 loop : 1.10 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.004 0.001 HIS A 287 PHE 0.017 0.002 PHE A 125 TYR 0.014 0.001 TYR A 42 ARG 0.003 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: B 74 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6607 (pp20) outliers start: 22 outliers final: 9 residues processed: 111 average time/residue: 1.2669 time to fit residues: 146.7899 Evaluate side-chains 102 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 94 ASN B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.151388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122229 restraints weight = 5693.711| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.40 r_work: 0.3299 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5830 Z= 0.191 Angle : 0.506 6.569 7899 Z= 0.259 Chirality : 0.042 0.163 885 Planarity : 0.004 0.049 1005 Dihedral : 7.862 93.583 814 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.37 % Allowed : 21.63 % Favored : 75.00 % 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: 1.78 (0.33), residues: 703 helix: 1.61 (0.27), residues: 386 sheet: 0.09 (0.54), residues: 80 loop : 1.10 (0.45), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.003 0.001 HIS A 287 PHE 0.013 0.001 PHE A 125 TYR 0.013 0.001 TYR A 42 ARG 0.004 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6405 (tm-30) REVERT: B 74 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6558 (pp20) outliers start: 21 outliers final: 10 residues processed: 108 average time/residue: 1.2018 time to fit residues: 135.7588 Evaluate side-chains 108 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 82 GLN A 148 ASN B 89 HIS B 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.150367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121137 restraints weight = 5714.193| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.40 r_work: 0.3312 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5830 Z= 0.225 Angle : 0.518 6.630 7899 Z= 0.266 Chirality : 0.042 0.162 885 Planarity : 0.004 0.050 1005 Dihedral : 7.836 87.070 814 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.53 % Allowed : 21.96 % Favored : 74.52 % 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: 1.72 (0.33), residues: 703 helix: 1.58 (0.27), residues: 386 sheet: 0.02 (0.54), residues: 80 loop : 1.06 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 277 HIS 0.003 0.001 HIS A 287 PHE 0.015 0.001 PHE A 125 TYR 0.014 0.001 TYR A 42 ARG 0.004 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: A 223 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: A 347 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7377 (ptmt) REVERT: B 74 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6506 (pp20) outliers start: 22 outliers final: 11 residues processed: 109 average time/residue: 1.4149 time to fit residues: 160.8280 Evaluate side-chains 107 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 148 ASN B 94 ASN B 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.151354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122449 restraints weight = 5756.575| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.38 r_work: 0.3284 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5830 Z= 0.246 Angle : 0.527 6.662 7899 Z= 0.272 Chirality : 0.043 0.156 885 Planarity : 0.004 0.050 1005 Dihedral : 7.872 83.620 814 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.85 % Allowed : 21.79 % Favored : 74.36 % 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: 1.68 (0.33), residues: 703 helix: 1.53 (0.27), residues: 386 sheet: 0.17 (0.57), residues: 73 loop : 1.00 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 277 HIS 0.004 0.001 HIS A 287 PHE 0.016 0.001 PHE A 125 TYR 0.014 0.001 TYR A 42 ARG 0.004 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: A 223 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6969 (mm-30) REVERT: A 347 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7398 (ptmt) REVERT: B 74 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6504 (pp20) REVERT: B 119 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7524 (mt-10) outliers start: 24 outliers final: 13 residues processed: 111 average time/residue: 1.5331 time to fit residues: 177.6596 Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 148 ASN B 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.153299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125752 restraints weight = 5671.763| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.30 r_work: 0.3295 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5830 Z= 0.237 Angle : 0.528 6.643 7899 Z= 0.272 Chirality : 0.043 0.161 885 Planarity : 0.004 0.050 1005 Dihedral : 7.849 80.337 814 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.53 % Allowed : 22.76 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.33), residues: 703 helix: 1.52 (0.27), residues: 386 sheet: 0.15 (0.57), residues: 73 loop : 0.96 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.005 0.001 HIS A 260 PHE 0.015 0.001 PHE A 125 TYR 0.014 0.001 TYR A 42 ARG 0.004 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: A 223 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6961 (mm-30) REVERT: A 347 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7390 (ptmt) REVERT: B 74 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6499 (pp20) REVERT: B 97 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7172 (mtp180) REVERT: B 119 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7519 (mt-10) REVERT: B 185 ARG cc_start: 0.7716 (tpp80) cc_final: 0.7485 (tpp80) outliers start: 22 outliers final: 13 residues processed: 109 average time/residue: 1.3715 time to fit residues: 156.1947 Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 20 optimal weight: 0.0470 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN B 94 ASN B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.153668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125041 restraints weight = 5718.445| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.39 r_work: 0.3301 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5830 Z= 0.184 Angle : 0.508 6.562 7899 Z= 0.261 Chirality : 0.041 0.155 885 Planarity : 0.004 0.049 1005 Dihedral : 7.565 75.161 814 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.53 % Allowed : 23.08 % Favored : 73.40 % 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: 1.70 (0.33), residues: 703 helix: 1.59 (0.27), residues: 387 sheet: 0.12 (0.54), residues: 79 loop : 0.94 (0.45), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 277 HIS 0.005 0.001 HIS A 260 PHE 0.013 0.001 PHE A 125 TYR 0.013 0.001 TYR A 42 ARG 0.004 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6974 (mm-30) REVERT: A 347 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7331 (ptmt) REVERT: B 74 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6518 (pp20) REVERT: B 97 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7152 (mtp180) REVERT: B 119 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7477 (mt-10) REVERT: B 185 ARG cc_start: 0.7704 (tpp80) cc_final: 0.7461 (tpp80) outliers start: 22 outliers final: 10 residues processed: 108 average time/residue: 1.5086 time to fit residues: 170.5413 Evaluate side-chains 107 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.0060 chunk 23 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.153934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125076 restraints weight = 5726.777| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.39 r_work: 0.3341 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5830 Z= 0.181 Angle : 0.508 6.489 7899 Z= 0.260 Chirality : 0.041 0.148 885 Planarity : 0.004 0.049 1005 Dihedral : 7.450 68.426 814 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.40 % Allowed : 24.04 % Favored : 73.56 % 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: 1.72 (0.33), residues: 703 helix: 1.59 (0.27), residues: 387 sheet: 0.10 (0.55), residues: 79 loop : 0.98 (0.45), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.003 0.001 HIS A 260 PHE 0.013 0.001 PHE A 125 TYR 0.013 0.001 TYR A 42 ARG 0.004 0.000 ARG B 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: A 347 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7346 (ptmt) REVERT: B 74 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6485 (pp20) REVERT: B 97 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7129 (mtp180) REVERT: B 119 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7477 (mt-10) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 1.3488 time to fit residues: 146.2103 Evaluate side-chains 105 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 0.0050 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.0020 chunk 16 optimal weight: 2.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.153818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124951 restraints weight = 5756.609| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.40 r_work: 0.3363 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5830 Z= 0.195 Angle : 0.519 6.422 7899 Z= 0.267 Chirality : 0.042 0.162 885 Planarity : 0.004 0.049 1005 Dihedral : 7.461 63.724 814 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.56 % Allowed : 24.04 % Favored : 73.40 % 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: 1.69 (0.33), residues: 703 helix: 1.58 (0.27), residues: 387 sheet: 0.08 (0.55), residues: 79 loop : 0.97 (0.45), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.007 0.001 HIS A 260 PHE 0.013 0.001 PHE A 125 TYR 0.014 0.001 TYR A 256 ARG 0.005 0.000 ARG B 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5143.28 seconds wall clock time: 91 minutes 0.49 seconds (5460.49 seconds total)