Starting phenix.real_space_refine on Mon Feb 10 19:52:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wqk_21871/02_2025/6wqk_21871.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wqk_21871/02_2025/6wqk_21871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wqk_21871/02_2025/6wqk_21871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wqk_21871/02_2025/6wqk_21871.map" model { file = "/net/cci-nas-00/data/ceres_data/6wqk_21871/02_2025/6wqk_21871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wqk_21871/02_2025/6wqk_21871.cif" } resolution = 3.1 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1255 2.51 5 N 370 2.21 5 O 435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2070 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Restraints were copied for chains: C, B, E, D Time building chain proxies: 1.21, per 1000 atoms: 0.58 Number of scatterers: 2070 At special positions: 0 Unit cell: (47.88, 79.8, 42.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 435 8.00 N 370 7.00 C 1255 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: 0.39 Conformation dependent library (CDL) restraints added in 851.1 milliseconds 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 274 through 277 removed outlier: 5.980A pdb=" N GLY B 274 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASN C 277 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 276 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A 274 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN B 277 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP A 276 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY D 274 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN E 277 " --> pdb=" O GLY D 274 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP D 276 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 288 through 290 removed outlier: 6.245A pdb=" N ASN A 289 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 304 through 306 removed outlier: 6.364A pdb=" N MET A 304 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 312 through 314 removed outlier: 6.700A pdb=" N ARG A 313 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG D 313 " --> pdb=" O ASN E 314 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 57 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: 0.42 Time building geometry restraints manager: 0.46 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: 730 1.34 - 1.46: 602 1.46 - 1.57: 783 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 2135 Sorted by residual: bond pdb=" CA GLN E 297 " pdb=" C GLN E 297 " ideal model delta sigma weight residual 1.524 1.533 -0.010 1.26e-02 6.30e+03 5.84e-01 bond pdb=" CA GLN A 297 " pdb=" C GLN A 297 " ideal model delta sigma weight residual 1.524 1.533 -0.010 1.26e-02 6.30e+03 5.80e-01 bond pdb=" CA GLN C 297 " pdb=" C GLN C 297 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.26e-02 6.30e+03 5.27e-01 bond pdb=" CA GLN B 297 " pdb=" C GLN B 297 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.26e-02 6.30e+03 5.19e-01 bond pdb=" CA GLN D 297 " pdb=" C GLN D 297 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.26e-02 6.30e+03 5.16e-01 ... (remaining 2130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 2558 1.04 - 2.09: 240 2.09 - 3.13: 47 3.13 - 4.17: 10 4.17 - 5.22: 5 Bond angle restraints: 2860 Sorted by residual: angle pdb=" N GLY B 292 " pdb=" CA GLY B 292 " pdb=" C GLY B 292 " ideal model delta sigma weight residual 112.02 117.24 -5.22 1.86e+00 2.89e-01 7.87e+00 angle pdb=" N GLY A 292 " pdb=" CA GLY A 292 " pdb=" C GLY A 292 " ideal model delta sigma weight residual 112.02 117.23 -5.21 1.86e+00 2.89e-01 7.85e+00 angle pdb=" N GLY C 292 " pdb=" CA GLY C 292 " pdb=" C GLY C 292 " ideal model delta sigma weight residual 112.02 117.23 -5.21 1.86e+00 2.89e-01 7.84e+00 angle pdb=" N GLY E 292 " pdb=" CA GLY E 292 " pdb=" C GLY E 292 " ideal model delta sigma weight residual 112.02 117.23 -5.21 1.86e+00 2.89e-01 7.84e+00 angle pdb=" N GLY D 292 " pdb=" CA GLY D 292 " pdb=" C GLY D 292 " ideal model delta sigma weight residual 112.02 117.21 -5.19 1.86e+00 2.89e-01 7.78e+00 ... (remaining 2855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.51: 950 13.51 - 27.03: 110 27.03 - 40.54: 30 40.54 - 54.05: 10 54.05 - 67.57: 10 Dihedral angle restraints: 1110 sinusoidal: 415 harmonic: 695 Sorted by residual: dihedral pdb=" CA ASN E 289 " pdb=" CB ASN E 289 " pdb=" CG ASN E 289 " pdb=" OD1 ASN E 289 " ideal model delta sinusoidal sigma weight residual -90.00 -157.57 67.57 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN C 289 " pdb=" CB ASN C 289 " pdb=" CG ASN C 289 " pdb=" OD1 ASN C 289 " ideal model delta sinusoidal sigma weight residual -90.00 -157.55 67.55 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN D 289 " pdb=" CB ASN D 289 " pdb=" CG ASN D 289 " pdb=" OD1 ASN D 289 " ideal model delta sinusoidal sigma weight residual -90.00 -157.52 67.52 2 2.00e+01 2.50e-03 1.02e+01 ... (remaining 1107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 80 0.020 - 0.041: 47 0.041 - 0.061: 42 0.061 - 0.081: 6 0.081 - 0.101: 10 Chirality restraints: 185 Sorted by residual: chirality pdb=" CA GLN B 297 " pdb=" N GLN B 297 " pdb=" C GLN B 297 " pdb=" CB GLN B 297 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.56e-01 chirality pdb=" CA GLN C 297 " pdb=" N GLN C 297 " pdb=" C GLN C 297 " pdb=" CB GLN C 297 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.55e-01 chirality pdb=" CA GLN A 297 " pdb=" N GLN A 297 " pdb=" C GLN A 297 " pdb=" CB GLN A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.49e-01 ... (remaining 182 not shown) Planarity restraints: 430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 300 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C ASN B 300 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN B 300 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR B 301 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 300 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C ASN A 300 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN A 300 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 301 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 300 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ASN C 300 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN C 300 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR C 301 " 0.009 2.00e-02 2.50e+03 ... (remaining 427 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 652 2.80 - 3.32: 1727 3.32 - 3.85: 3702 3.85 - 4.37: 4452 4.37 - 4.90: 7957 Nonbonded interactions: 18490 Sorted by model distance: nonbonded pdb=" O SER A 285 " pdb=" OG SER B 306 " model vdw 2.272 3.040 nonbonded pdb=" O SER D 285 " pdb=" OG SER E 306 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A 306 " pdb=" O SER E 285 " model vdw 2.330 3.040 nonbonded pdb=" ND2 ASN A 295 " pdb=" O PHE B 291 " model vdw 2.364 3.120 nonbonded pdb=" O SER B 285 " pdb=" OG SER C 306 " model vdw 2.373 3.040 ... (remaining 18485 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.090 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 0.011 2135 Z= 0.208 Angle : 0.701 5.217 2860 Z= 0.405 Chirality : 0.039 0.101 185 Planarity : 0.004 0.015 430 Dihedral : 14.473 67.565 740 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % 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: -5.40 (0.23), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.17), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE A 309 TYR 0.007 0.001 TYR E 301 ARG 0.000 0.000 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.201 Fit side-chains REVERT: B 305 LYS cc_start: 0.8442 (tttt) cc_final: 0.8145 (ttpp) REVERT: E 294 TYR cc_start: 0.8439 (m-80) cc_final: 0.7825 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1186 time to fit residues: 3.5353 Evaluate side-chains 24 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.120716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095482 restraints weight = 2379.640| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.01 r_work: 0.3209 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 2135 Z= 0.382 Angle : 0.582 4.034 2860 Z= 0.308 Chirality : 0.047 0.115 185 Planarity : 0.004 0.033 430 Dihedral : 5.003 15.653 330 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.08 % Allowed : 10.27 % Favored : 88.65 % 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: -4.79 (0.26), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.20), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.004 PHE D 309 TYR 0.011 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.217 Fit side-chains REVERT: D 297 GLN cc_start: 0.8932 (mp10) cc_final: 0.8672 (mp10) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.1452 time to fit residues: 4.9403 Evaluate side-chains 30 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain C residue 304 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.119788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.094376 restraints weight = 2357.517| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.03 r_work: 0.3197 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2135 Z= 0.352 Angle : 0.571 4.832 2860 Z= 0.300 Chirality : 0.046 0.113 185 Planarity : 0.004 0.032 430 Dihedral : 4.859 14.897 330 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.08 % Allowed : 9.19 % Favored : 89.73 % 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: -4.51 (0.27), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.21), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE D 309 TYR 0.011 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.225 Fit side-chains REVERT: A 297 GLN cc_start: 0.8847 (mp10) cc_final: 0.8646 (mp10) REVERT: D 297 GLN cc_start: 0.9010 (mp10) cc_final: 0.8635 (mp10) outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.1306 time to fit residues: 5.1794 Evaluate side-chains 33 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.119636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092752 restraints weight = 2305.963| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.96 r_work: 0.3223 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2135 Z= 0.275 Angle : 0.545 4.374 2860 Z= 0.284 Chirality : 0.044 0.104 185 Planarity : 0.004 0.029 430 Dihedral : 4.603 14.444 330 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.08 % Allowed : 9.73 % Favored : 89.19 % 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: -4.41 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.21), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE D 309 TYR 0.011 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.195 Fit side-chains REVERT: D 297 GLN cc_start: 0.8999 (mp10) cc_final: 0.8621 (mp10) outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.1189 time to fit residues: 4.7891 Evaluate side-chains 34 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN E 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.118706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091881 restraints weight = 2341.191| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.98 r_work: 0.3206 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2135 Z= 0.302 Angle : 0.565 5.260 2860 Z= 0.294 Chirality : 0.045 0.123 185 Planarity : 0.004 0.031 430 Dihedral : 4.594 14.271 330 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.08 % Allowed : 10.27 % Favored : 88.65 % 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: -4.37 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.21), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE D 309 TYR 0.011 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.173 Fit side-chains REVERT: D 297 GLN cc_start: 0.9004 (mp10) cc_final: 0.8744 (mp10) outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.1192 time to fit residues: 4.9796 Evaluate side-chains 35 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.120592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093579 restraints weight = 2266.290| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.99 r_work: 0.3237 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2135 Z= 0.240 Angle : 0.549 5.881 2860 Z= 0.283 Chirality : 0.044 0.134 185 Planarity : 0.003 0.028 430 Dihedral : 4.393 14.355 330 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.08 % Allowed : 11.35 % Favored : 87.57 % 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: -4.38 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.21), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE D 309 TYR 0.010 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.204 Fit side-chains REVERT: D 297 GLN cc_start: 0.8968 (mp10) cc_final: 0.8642 (mp10) outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.1198 time to fit residues: 4.9899 Evaluate side-chains 35 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 0.0870 chunk 6 optimal weight: 7.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.119355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.092283 restraints weight = 2335.591| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.99 r_work: 0.3219 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2135 Z= 0.288 Angle : 0.586 6.521 2860 Z= 0.305 Chirality : 0.045 0.151 185 Planarity : 0.004 0.030 430 Dihedral : 4.525 14.665 330 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.08 % Allowed : 12.43 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.40 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE D 309 TYR 0.011 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.190 Fit side-chains REVERT: D 297 GLN cc_start: 0.8977 (mp10) cc_final: 0.8680 (mp10) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.1411 time to fit residues: 6.1496 Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.120640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093346 restraints weight = 2340.865| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.03 r_work: 0.3232 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2135 Z= 0.233 Angle : 0.561 5.400 2860 Z= 0.289 Chirality : 0.044 0.120 185 Planarity : 0.003 0.028 430 Dihedral : 4.395 14.363 330 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.08 % Allowed : 12.43 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.39 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE D 309 TYR 0.010 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.209 Fit side-chains REVERT: D 297 GLN cc_start: 0.8972 (mp10) cc_final: 0.8588 (mp10) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.1192 time to fit residues: 5.2590 Evaluate side-chains 37 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 0.0970 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096643 restraints weight = 2342.412| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.02 r_work: 0.3290 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 2135 Z= 0.163 Angle : 0.554 5.514 2860 Z= 0.283 Chirality : 0.043 0.125 185 Planarity : 0.003 0.023 430 Dihedral : 4.068 13.459 330 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.54 % Allowed : 12.97 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.38 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE D 291 TYR 0.009 0.001 TYR D 301 ARG 0.002 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.228 Fit side-chains REVERT: D 297 GLN cc_start: 0.8920 (mp10) cc_final: 0.8672 (mp10) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.1130 time to fit residues: 5.0793 Evaluate side-chains 36 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 18 optimal weight: 0.0970 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.120663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093518 restraints weight = 2329.846| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.00 r_work: 0.3244 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2135 Z= 0.276 Angle : 0.606 6.138 2860 Z= 0.314 Chirality : 0.045 0.132 185 Planarity : 0.003 0.028 430 Dihedral : 4.463 14.872 330 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.08 % Allowed : 12.43 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.35 (0.29), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE D 309 TYR 0.010 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.202 Fit side-chains REVERT: D 297 GLN cc_start: 0.8976 (mp10) cc_final: 0.8687 (mp10) outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.1244 time to fit residues: 5.1208 Evaluate side-chains 36 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.094448 restraints weight = 2337.324| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.01 r_work: 0.3259 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2135 Z= 0.240 Angle : 0.597 6.166 2860 Z= 0.309 Chirality : 0.045 0.131 185 Planarity : 0.003 0.027 430 Dihedral : 4.392 14.870 330 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.54 % Allowed : 12.97 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.37 (0.29), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.22), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE D 309 TYR 0.010 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 =============================================================================== Job complete usr+sys time: 1344.60 seconds wall clock time: 24 minutes 46.34 seconds (1486.34 seconds total)