Starting phenix.real_space_refine on Wed Mar 5 14:43:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wqk_21871/03_2025/6wqk_21871.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wqk_21871/03_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_21871/03_2025/6wqk_21871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wqk_21871/03_2025/6wqk_21871.map" model { file = "/net/cci-nas-00/data/ceres_data/6wqk_21871/03_2025/6wqk_21871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wqk_21871/03_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-5624/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: 1.18, per 1000 atoms: 0.57 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: 0.54 Conformation dependent library (CDL) restraints added in 285.7 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: 0.24 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: 0.47 Time building geometry restraints manager: 0.64 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: 0.160 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.160 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.580 ------------------------------------------------------------------------------- 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 : 0.213 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: 0.1153 time to fit residues: 3.4617 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 : 0.186 ------------------------------------------------------------------------------- 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: 3.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.121269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096011 restraints weight = 2369.807| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.02 r_work: 0.3215 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1368 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= 0.346 Angle : 0.570 4.070 2860 Z= 0.301 Chirality : 0.046 0.110 185 Planarity : 0.004 0.032 430 Dihedral : 4.931 15.334 330 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.67 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: -4.80 (0.26), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.19), 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 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 : 0.202 Fit side-chains REVERT: D 297 GLN cc_start: 0.8925 (mp10) cc_final: 0.8659 (mp10) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.1289 time to fit residues: 4.4183 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 : 0.194 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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** 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 = 0.3663 r_free = 0.3663 target = 0.118397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092996 restraints weight = 2368.107| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.02 r_work: 0.3175 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1878 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= 0.426 Angle : 0.601 4.508 2860 Z= 0.318 Chirality : 0.047 0.118 185 Planarity : 0.005 0.036 430 Dihedral : 5.039 15.173 330 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: -4.48 (0.27), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.21), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.004 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 35 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.194 Fit side-chains REVERT: D 297 GLN cc_start: 0.9008 (mp10) cc_final: 0.8686 (mp10) outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.1651 time to fit residues: 6.4040 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 : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain E residue 299 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 0.0030 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- 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 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 = 0.3748 r_free = 0.3748 target = 0.125217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097851 restraints weight = 2242.701| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.00 r_work: 0.3300 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2135 Z= 0.127 Angle : 0.508 5.892 2860 Z= 0.258 Chirality : 0.042 0.118 185 Planarity : 0.003 0.029 430 Dihedral : 4.065 12.463 330 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.54 % Allowed : 10.27 % 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: -4.50 (0.27), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.21), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE A 309 TYR 0.009 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: 1 poor density : 34 time to evaluate : 0.188 Fit side-chains REVERT: D 297 GLN cc_start: 0.8880 (mp10) cc_final: 0.8530 (mp10) outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.1451 time to fit residues: 5.8302 Evaluate side-chains 35 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 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 = 0.3646 r_free = 0.3646 target = 0.117580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090918 restraints weight = 2350.018| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.96 r_work: 0.3188 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2152 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= 0.388 Angle : 0.596 4.918 2860 Z= 0.314 Chirality : 0.046 0.125 185 Planarity : 0.005 0.044 430 Dihedral : 4.770 14.735 330 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.54 % Allowed : 10.81 % 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: -4.35 (0.28), residues: 275 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.21), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 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 35 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.212 Fit side-chains REVERT: D 297 GLN cc_start: 0.9013 (mp10) cc_final: 0.8734 (mp10) outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.1226 time to fit residues: 5.1300 Evaluate side-chains 34 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 5 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** D 295 ASN E 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.121153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.094075 restraints weight = 2271.140| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.00 r_work: 0.3245 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2135 Z= 0.209 Angle : 0.538 5.542 2860 Z= 0.276 Chirality : 0.043 0.112 185 Planarity : 0.003 0.031 430 Dihedral : 4.343 13.519 330 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.08 % Allowed : 11.89 % Favored : 87.03 % 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 0.008 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 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: 0.8944 (mp10) cc_final: 0.8532 (mp10) outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.1185 time to fit residues: 4.7974 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 : 0.185 ------------------------------------------------------------------------------- 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: 9.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.117595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090746 restraints weight = 2363.310| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.99 r_work: 0.3191 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2135 Z= 0.360 Angle : 0.615 6.360 2860 Z= 0.322 Chirality : 0.046 0.130 185 Planarity : 0.004 0.038 430 Dihedral : 4.760 15.054 330 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.62 % Allowed : 11.89 % 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 (0.28), 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 0.014 0.003 PHE D 309 TYR 0.011 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 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 37 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.210 Fit side-chains REVERT: D 297 GLN cc_start: 0.8989 (mp10) cc_final: 0.8669 (mp10) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.1231 time to fit residues: 5.1151 Evaluate side-chains 37 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain D residue 304 MET 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: 3.9990 chunk 3 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.120655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093270 restraints weight = 2343.757| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.02 r_work: 0.3233 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2135 Z= 0.242 Angle : 0.572 5.549 2860 Z= 0.294 Chirality : 0.044 0.127 185 Planarity : 0.004 0.032 430 Dihedral : 4.463 14.304 330 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.62 % Allowed : 11.89 % 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 (0.28), 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 0.010 0.002 PHE D 309 TYR 0.010 0.001 TYR D 301 ARG 0.002 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 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 37 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.204 Fit side-chains REVERT: D 297 GLN cc_start: 0.8935 (mp10) cc_final: 0.8667 (mp10) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.1196 time to fit residues: 4.9878 Evaluate side-chains 36 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain D residue 304 MET 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: 8.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 0.0040 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.123179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095723 restraints weight = 2346.631| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.03 r_work: 0.3278 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.003 0.031 2135 Z= 0.183 Angle : 0.568 5.751 2860 Z= 0.291 Chirality : 0.043 0.126 185 Planarity : 0.003 0.028 430 Dihedral : 4.190 13.788 330 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.62 % Allowed : 11.89 % 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 (0.28), 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 309 TYR 0.009 0.001 TYR D 301 ARG 0.002 0.001 ARG B 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: 3 poor density : 34 time to evaluate : 0.168 Fit side-chains REVERT: D 297 GLN cc_start: 0.8934 (mp10) cc_final: 0.8675 (mp10) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.1457 time to fit residues: 6.1192 Evaluate side-chains 36 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER 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 18 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.120500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093112 restraints weight = 2335.425| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.02 r_work: 0.3241 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2465 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= 0.286 Angle : 0.615 6.099 2860 Z= 0.319 Chirality : 0.046 0.137 185 Planarity : 0.004 0.033 430 Dihedral : 4.528 15.192 330 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.62 % Allowed : 12.43 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.011 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 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.534 Fit side-chains REVERT: D 297 GLN cc_start: 0.8974 (mp10) cc_final: 0.8680 (mp10) outliers start: 3 outliers final: 3 residues processed: 35 average time/residue: 0.1282 time to fit residues: 5.5299 Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 SER 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: 10.0000 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.124537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096795 restraints weight = 2310.147| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.03 r_work: 0.3292 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2135 Z= 0.185 Angle : 0.583 6.193 2860 Z= 0.299 Chirality : 0.043 0.127 185 Planarity : 0.003 0.027 430 Dihedral : 4.099 14.115 330 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.62 % Allowed : 12.43 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.006 0.002 PHE E 291 TYR 0.009 0.001 TYR D 301 ARG 0.002 0.001 ARG D 313 =============================================================================== Job complete usr+sys time: 1452.73 seconds wall clock time: 25 minutes 45.78 seconds (1545.78 seconds total)