Starting phenix.real_space_refine on Tue Feb 11 06:28:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cz6_30507/02_2025/7cz6_30507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cz6_30507/02_2025/7cz6_30507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cz6_30507/02_2025/7cz6_30507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cz6_30507/02_2025/7cz6_30507.map" model { file = "/net/cci-nas-00/data/ceres_data/7cz6_30507/02_2025/7cz6_30507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cz6_30507/02_2025/7cz6_30507.cif" } resolution = 4.1 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 20 5.16 5 C 2900 2.51 5 N 700 2.21 5 O 915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4535 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 116} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.08, per 1000 atoms: 0.46 Number of scatterers: 4535 At special positions: 0 Unit cell: (71.94, 71.94, 90.47, 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 20 16.00 O 915 8.00 N 700 7.00 C 2900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 532.6 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing sheet with id=1, first strand: chain 'C' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR C 275 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 318 " --> pdb=" O TYR C 275 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'C' and resid 262 through 264 Processing sheet with id=3, first strand: chain 'A' and resid 248 through 254 removed outlier: 5.248A pdb=" N TYR A 275 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 318 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 262 through 264 Processing sheet with id=5, first strand: chain 'B' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR B 275 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 318 " --> pdb=" O TYR B 275 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=7, first strand: chain 'D' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR D 275 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 318 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 262 through 264 Processing sheet with id=9, first strand: chain 'E' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR E 275 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR E 318 " --> pdb=" O TYR E 275 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 262 through 264 150 hydrogen bonds defined for protein. 405 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: 1.38 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1362 1.34 - 1.46: 960 1.46 - 1.58: 2288 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 4640 Sorted by residual: bond pdb=" CA PRO E 269 " pdb=" C PRO E 269 " ideal model delta sigma weight residual 1.520 1.556 -0.036 1.42e-02 4.96e+03 6.45e+00 bond pdb=" CA PRO B 269 " pdb=" C PRO B 269 " ideal model delta sigma weight residual 1.520 1.556 -0.036 1.42e-02 4.96e+03 6.43e+00 bond pdb=" CA PRO C 269 " pdb=" C PRO C 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.38e+00 bond pdb=" CA PRO D 269 " pdb=" C PRO D 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.37e+00 bond pdb=" CA PRO A 269 " pdb=" C PRO A 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.37e+00 ... (remaining 4635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 5874 2.75 - 5.50: 426 5.50 - 8.25: 90 8.25 - 11.00: 5 11.00 - 13.75: 5 Bond angle restraints: 6400 Sorted by residual: angle pdb=" N TYR D 304 " pdb=" CA TYR D 304 " pdb=" C TYR D 304 " ideal model delta sigma weight residual 107.60 121.35 -13.75 1.83e+00 2.99e-01 5.65e+01 angle pdb=" N TYR B 304 " pdb=" CA TYR B 304 " pdb=" C TYR B 304 " ideal model delta sigma weight residual 107.60 121.34 -13.74 1.83e+00 2.99e-01 5.64e+01 angle pdb=" N TYR C 304 " pdb=" CA TYR C 304 " pdb=" C TYR C 304 " ideal model delta sigma weight residual 107.60 121.32 -13.72 1.83e+00 2.99e-01 5.62e+01 angle pdb=" N TYR A 304 " pdb=" CA TYR A 304 " pdb=" C TYR A 304 " ideal model delta sigma weight residual 107.60 121.31 -13.71 1.83e+00 2.99e-01 5.62e+01 angle pdb=" N TYR E 304 " pdb=" CA TYR E 304 " pdb=" C TYR E 304 " ideal model delta sigma weight residual 107.60 121.31 -13.71 1.83e+00 2.99e-01 5.61e+01 ... (remaining 6395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 2527 11.99 - 23.97: 123 23.97 - 35.95: 10 35.95 - 47.94: 15 47.94 - 59.92: 5 Dihedral angle restraints: 2680 sinusoidal: 900 harmonic: 1780 Sorted by residual: dihedral pdb=" CA GLY D 317 " pdb=" C GLY D 317 " pdb=" N THR D 318 " pdb=" CA THR D 318 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLY B 317 " pdb=" C GLY B 317 " pdb=" N THR B 318 " pdb=" CA THR B 318 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLY E 317 " pdb=" C GLY E 317 " pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 2677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 702 0.061 - 0.122: 107 0.122 - 0.182: 11 0.182 - 0.243: 0 0.243 - 0.304: 5 Chirality restraints: 825 Sorted by residual: chirality pdb=" CA TYR E 304 " pdb=" N TYR E 304 " pdb=" C TYR E 304 " pdb=" CB TYR E 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA TYR D 304 " pdb=" N TYR D 304 " pdb=" C TYR D 304 " pdb=" CB TYR D 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA TYR C 304 " pdb=" N TYR C 304 " pdb=" C TYR C 304 " pdb=" CB TYR C 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 822 not shown) Planarity restraints: 795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 268 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO D 269 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 268 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO C 269 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 260 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO B 261 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.037 5.00e-02 4.00e+02 ... (remaining 792 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 15 1.82 - 2.59: 135 2.59 - 3.36: 6419 3.36 - 4.13: 10246 4.13 - 4.90: 17972 Nonbonded interactions: 34787 Sorted by model distance: nonbonded pdb=" O ASP A 309 " pdb=" OD2 ASP B 309 " model vdw 1.047 3.040 nonbonded pdb=" O ASP B 309 " pdb=" OD2 ASP D 309 " model vdw 1.047 3.040 nonbonded pdb=" O ASP C 309 " pdb=" OD2 ASP A 309 " model vdw 1.048 3.040 nonbonded pdb=" OD2 ASP C 309 " pdb=" O ASP E 309 " model vdw 1.048 3.040 nonbonded pdb=" O ASP D 309 " pdb=" OD2 ASP E 309 " model vdw 1.048 3.040 ... (remaining 34782 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: 0.04 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 group one per residue 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: 0.080 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.750 Find NCS groups from input model: 0.090 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:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 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 : 0.009 0.041 4640 Z= 0.576 Angle : 1.616 13.750 6400 Z= 1.065 Chirality : 0.052 0.304 825 Planarity : 0.008 0.062 795 Dihedral : 8.570 59.920 1540 Min Nonbonded Distance : 1.047 Molprobity Statistics. All-atom Clashscore : 61.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.79 (0.37), residues: 180 loop : -1.29 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 331 PHE 0.010 0.002 PHE E 307 TYR 0.008 0.001 TYR B 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 THR cc_start: 0.7462 (p) cc_final: 0.6956 (p) REVERT: A 277 THR cc_start: 0.7645 (p) cc_final: 0.7384 (p) REVERT: A 341 MET cc_start: 0.7260 (tpp) cc_final: 0.6909 (tpp) REVERT: B 277 THR cc_start: 0.7265 (p) cc_final: 0.6680 (p) REVERT: D 277 THR cc_start: 0.7581 (p) cc_final: 0.7104 (p) REVERT: D 348 LYS cc_start: 0.7769 (mttt) cc_final: 0.7324 (mttt) REVERT: E 348 LYS cc_start: 0.7677 (mttt) cc_final: 0.7329 (mttt) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1202 time to fit residues: 38.5820 Evaluate side-chains 170 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN A 282 GLN A 305 GLN A 360 GLN B 276 GLN B 305 GLN B 360 GLN D 305 GLN D 360 GLN E 305 GLN E 360 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.170915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123720 restraints weight = 8751.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127953 restraints weight = 5369.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130818 restraints weight = 3857.180| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4640 Z= 0.366 Angle : 0.816 8.334 6400 Z= 0.448 Chirality : 0.053 0.155 825 Planarity : 0.007 0.055 795 Dihedral : 7.890 26.092 640 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.99 (0.34), residues: 245 loop : -1.65 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 331 PHE 0.024 0.003 PHE D 307 TYR 0.015 0.002 TYR D 275 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 275 TYR cc_start: 0.8523 (m-80) cc_final: 0.8132 (m-80) REVERT: C 276 GLN cc_start: 0.8410 (tt0) cc_final: 0.7398 (tt0) REVERT: C 284 LEU cc_start: 0.9288 (mt) cc_final: 0.9018 (mt) REVERT: C 311 PHE cc_start: 0.9208 (t80) cc_final: 0.8849 (t80) REVERT: C 318 THR cc_start: 0.8767 (p) cc_final: 0.8519 (p) REVERT: A 275 TYR cc_start: 0.8511 (m-80) cc_final: 0.8147 (m-80) REVERT: A 284 LEU cc_start: 0.9197 (mt) cc_final: 0.8893 (mt) REVERT: A 311 PHE cc_start: 0.9314 (t80) cc_final: 0.9014 (t80) REVERT: B 262 GLN cc_start: 0.8366 (pp30) cc_final: 0.7686 (pp30) REVERT: B 264 LEU cc_start: 0.9041 (pp) cc_final: 0.8714 (mm) REVERT: B 275 TYR cc_start: 0.8447 (m-80) cc_final: 0.7941 (m-80) REVERT: B 311 PHE cc_start: 0.9321 (t80) cc_final: 0.8873 (t80) REVERT: B 340 THR cc_start: 0.7890 (p) cc_final: 0.7520 (p) REVERT: D 275 TYR cc_start: 0.8435 (m-80) cc_final: 0.8070 (m-80) REVERT: D 284 LEU cc_start: 0.9032 (mt) cc_final: 0.8798 (mt) REVERT: D 339 LEU cc_start: 0.8391 (mt) cc_final: 0.8189 (mt) REVERT: D 340 THR cc_start: 0.7779 (p) cc_final: 0.7392 (p) REVERT: E 275 TYR cc_start: 0.8446 (m-80) cc_final: 0.8073 (m-80) REVERT: E 340 THR cc_start: 0.7744 (p) cc_final: 0.7394 (p) outliers start: 1 outliers final: 1 residues processed: 229 average time/residue: 0.1317 time to fit residues: 39.7013 Evaluate side-chains 194 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN C 305 GLN A 276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.167645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117398 restraints weight = 9193.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.121031 restraints weight = 5732.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123785 restraints weight = 4272.843| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 4640 Z= 0.320 Angle : 0.712 6.982 6400 Z= 0.390 Chirality : 0.048 0.164 825 Planarity : 0.006 0.058 795 Dihedral : 7.054 23.297 640 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.77 (0.36), residues: 245 loop : -1.79 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 331 PHE 0.016 0.002 PHE D 311 TYR 0.019 0.002 TYR E 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: C 275 TYR cc_start: 0.8468 (m-80) cc_final: 0.7720 (m-80) REVERT: C 276 GLN cc_start: 0.8963 (tt0) cc_final: 0.8762 (tt0) REVERT: C 308 ASP cc_start: 0.9073 (m-30) cc_final: 0.8846 (m-30) REVERT: C 311 PHE cc_start: 0.9265 (t80) cc_final: 0.8874 (t80) REVERT: C 318 THR cc_start: 0.9029 (p) cc_final: 0.8785 (p) REVERT: C 340 THR cc_start: 0.7876 (p) cc_final: 0.7566 (p) REVERT: A 262 GLN cc_start: 0.8005 (pp30) cc_final: 0.7618 (pp30) REVERT: A 264 LEU cc_start: 0.8967 (mt) cc_final: 0.8683 (mt) REVERT: A 275 TYR cc_start: 0.8289 (m-80) cc_final: 0.7430 (m-80) REVERT: A 308 ASP cc_start: 0.9149 (m-30) cc_final: 0.8937 (m-30) REVERT: A 311 PHE cc_start: 0.9394 (t80) cc_final: 0.9042 (t80) REVERT: A 339 LEU cc_start: 0.8408 (mt) cc_final: 0.8041 (mt) REVERT: B 262 GLN cc_start: 0.8317 (pp30) cc_final: 0.7686 (pp30) REVERT: B 264 LEU cc_start: 0.8992 (pp) cc_final: 0.8671 (mm) REVERT: B 308 ASP cc_start: 0.8926 (m-30) cc_final: 0.8689 (m-30) REVERT: B 311 PHE cc_start: 0.9191 (t80) cc_final: 0.8871 (t80) REVERT: B 339 LEU cc_start: 0.8522 (mt) cc_final: 0.8163 (mt) REVERT: B 340 THR cc_start: 0.7933 (p) cc_final: 0.7508 (p) REVERT: D 329 VAL cc_start: 0.9534 (t) cc_final: 0.9237 (t) REVERT: D 340 THR cc_start: 0.7902 (p) cc_final: 0.7581 (p) REVERT: E 308 ASP cc_start: 0.9103 (m-30) cc_final: 0.8750 (m-30) REVERT: E 318 THR cc_start: 0.8930 (p) cc_final: 0.8659 (p) REVERT: E 340 THR cc_start: 0.7858 (p) cc_final: 0.7224 (t) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1186 time to fit residues: 35.3892 Evaluate side-chains 196 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 0.0970 chunk 40 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN ** E 282 GLN ** 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 = 0.4052 r_free = 0.4052 target = 0.168744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116244 restraints weight = 9098.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119973 restraints weight = 5820.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122672 restraints weight = 4399.160| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4640 Z= 0.307 Angle : 0.683 6.570 6400 Z= 0.374 Chirality : 0.048 0.153 825 Planarity : 0.006 0.065 795 Dihedral : 6.773 23.909 640 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.34), residues: 620 helix: None (None), residues: 0 sheet: -0.72 (0.36), residues: 245 loop : -1.75 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 331 PHE 0.019 0.002 PHE B 297 TYR 0.019 0.002 TYR E 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.526 Fit side-chains REVERT: C 275 TYR cc_start: 0.8403 (m-80) cc_final: 0.7834 (m-80) REVERT: C 308 ASP cc_start: 0.8958 (m-30) cc_final: 0.8753 (m-30) REVERT: C 311 PHE cc_start: 0.9270 (t80) cc_final: 0.8862 (t80) REVERT: C 318 THR cc_start: 0.8985 (p) cc_final: 0.8757 (p) REVERT: C 340 THR cc_start: 0.7851 (p) cc_final: 0.7511 (p) REVERT: A 275 TYR cc_start: 0.8304 (m-80) cc_final: 0.7631 (m-80) REVERT: A 311 PHE cc_start: 0.9434 (t80) cc_final: 0.9060 (t80) REVERT: A 339 LEU cc_start: 0.8447 (mt) cc_final: 0.8207 (mt) REVERT: B 262 GLN cc_start: 0.8329 (pp30) cc_final: 0.7675 (pp30) REVERT: B 264 LEU cc_start: 0.9049 (pp) cc_final: 0.8714 (mm) REVERT: B 275 TYR cc_start: 0.8049 (m-80) cc_final: 0.7412 (m-80) REVERT: B 308 ASP cc_start: 0.9025 (m-30) cc_final: 0.8779 (m-30) REVERT: B 311 PHE cc_start: 0.9207 (t80) cc_final: 0.8907 (t80) REVERT: B 340 THR cc_start: 0.8144 (p) cc_final: 0.7764 (p) REVERT: D 308 ASP cc_start: 0.9051 (m-30) cc_final: 0.8831 (m-30) REVERT: D 340 THR cc_start: 0.7902 (p) cc_final: 0.7545 (p) REVERT: E 275 TYR cc_start: 0.8352 (m-80) cc_final: 0.7799 (m-80) REVERT: E 339 LEU cc_start: 0.8535 (mt) cc_final: 0.8305 (mt) REVERT: E 340 THR cc_start: 0.8036 (p) cc_final: 0.7337 (t) REVERT: E 348 LYS cc_start: 0.9390 (mtmm) cc_final: 0.8723 (mtmm) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1187 time to fit residues: 35.2526 Evaluate side-chains 199 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 0.0670 overall best weight: 1.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN D 253 ASN D 282 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.173979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121010 restraints weight = 8869.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124879 restraints weight = 5628.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127756 restraints weight = 4230.273| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4640 Z= 0.213 Angle : 0.673 7.536 6400 Z= 0.360 Chirality : 0.049 0.157 825 Planarity : 0.006 0.064 795 Dihedral : 6.463 22.975 640 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.19 % Allowed : 1.35 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.64 (0.34), residues: 245 loop : -1.69 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 331 PHE 0.020 0.002 PHE B 297 TYR 0.021 0.002 TYR B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: C 275 TYR cc_start: 0.8407 (m-80) cc_final: 0.8071 (m-80) REVERT: C 311 PHE cc_start: 0.9226 (t80) cc_final: 0.8741 (t80) REVERT: C 314 PHE cc_start: 0.8031 (m-80) cc_final: 0.7673 (m-10) REVERT: C 340 THR cc_start: 0.8040 (p) cc_final: 0.7731 (p) REVERT: A 251 PHE cc_start: 0.6586 (p90) cc_final: 0.6211 (p90) REVERT: A 266 MET cc_start: 0.5730 (mpp) cc_final: 0.5364 (mpp) REVERT: A 275 TYR cc_start: 0.8268 (m-80) cc_final: 0.7701 (m-80) REVERT: A 311 PHE cc_start: 0.9427 (t80) cc_final: 0.9053 (t80) REVERT: B 275 TYR cc_start: 0.8277 (m-80) cc_final: 0.7827 (m-80) REVERT: B 308 ASP cc_start: 0.9024 (m-30) cc_final: 0.8791 (m-30) REVERT: B 311 PHE cc_start: 0.9180 (t80) cc_final: 0.8774 (t80) REVERT: B 340 THR cc_start: 0.8470 (p) cc_final: 0.8131 (p) REVERT: D 262 GLN cc_start: 0.7018 (tp40) cc_final: 0.6597 (tp40) REVERT: D 314 PHE cc_start: 0.8170 (m-80) cc_final: 0.7911 (m-10) REVERT: D 340 THR cc_start: 0.8251 (p) cc_final: 0.7907 (p) REVERT: E 264 LEU cc_start: 0.8816 (mm) cc_final: 0.8609 (mm) REVERT: E 275 TYR cc_start: 0.8323 (m-80) cc_final: 0.7829 (m-80) REVERT: E 339 LEU cc_start: 0.8420 (mt) cc_final: 0.8157 (mt) REVERT: E 340 THR cc_start: 0.7939 (p) cc_final: 0.7251 (t) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.1180 time to fit residues: 36.5336 Evaluate side-chains 215 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 0.0010 chunk 57 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 overall best weight: 2.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN B 253 ASN B 282 GLN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.172561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122245 restraints weight = 8502.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126286 restraints weight = 5224.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129072 restraints weight = 3822.246| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4640 Z= 0.253 Angle : 0.656 7.244 6400 Z= 0.354 Chirality : 0.049 0.169 825 Planarity : 0.006 0.064 795 Dihedral : 6.399 22.023 640 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.57 (0.33), residues: 245 loop : -1.72 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 331 PHE 0.024 0.002 PHE B 314 TYR 0.011 0.001 TYR E 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.485 Fit side-chains REVERT: C 311 PHE cc_start: 0.9244 (t80) cc_final: 0.8773 (t80) REVERT: C 340 THR cc_start: 0.8168 (p) cc_final: 0.7848 (p) REVERT: A 251 PHE cc_start: 0.6609 (p90) cc_final: 0.6218 (p90) REVERT: A 266 MET cc_start: 0.5950 (mpp) cc_final: 0.5604 (mpp) REVERT: A 275 TYR cc_start: 0.8268 (m-80) cc_final: 0.7813 (m-80) REVERT: A 311 PHE cc_start: 0.9399 (t80) cc_final: 0.9003 (t80) REVERT: A 340 THR cc_start: 0.7876 (p) cc_final: 0.7564 (p) REVERT: A 348 LYS cc_start: 0.9363 (mtmm) cc_final: 0.8941 (mtmm) REVERT: B 275 TYR cc_start: 0.8300 (m-80) cc_final: 0.7937 (m-80) REVERT: B 311 PHE cc_start: 0.9231 (t80) cc_final: 0.8852 (t80) REVERT: B 340 THR cc_start: 0.8418 (p) cc_final: 0.8048 (p) REVERT: D 314 PHE cc_start: 0.8159 (m-80) cc_final: 0.7866 (m-80) REVERT: D 340 THR cc_start: 0.8133 (p) cc_final: 0.7772 (p) REVERT: E 275 TYR cc_start: 0.8492 (m-80) cc_final: 0.8199 (m-80) REVERT: E 339 LEU cc_start: 0.8460 (mt) cc_final: 0.8183 (mt) REVERT: E 340 THR cc_start: 0.8015 (p) cc_final: 0.7287 (t) REVERT: E 348 LYS cc_start: 0.9350 (mtmm) cc_final: 0.8878 (mtmm) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1257 time to fit residues: 37.7381 Evaluate side-chains 205 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 0.0470 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 31 optimal weight: 0.0570 chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN D 282 GLN E 256 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.177288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122991 restraints weight = 8635.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126991 restraints weight = 5558.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129778 restraints weight = 4198.186| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4640 Z= 0.230 Angle : 0.660 7.661 6400 Z= 0.351 Chirality : 0.050 0.166 825 Planarity : 0.006 0.066 795 Dihedral : 6.261 21.948 640 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.43 (0.33), residues: 245 loop : -1.76 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 331 PHE 0.039 0.002 PHE B 314 TYR 0.011 0.001 TYR E 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.921 Fit side-chains REVERT: C 311 PHE cc_start: 0.9215 (t80) cc_final: 0.8857 (t80) REVERT: C 314 PHE cc_start: 0.7854 (m-80) cc_final: 0.7448 (m-10) REVERT: C 340 THR cc_start: 0.8082 (p) cc_final: 0.7772 (p) REVERT: A 251 PHE cc_start: 0.6526 (p90) cc_final: 0.6079 (p90) REVERT: A 266 MET cc_start: 0.5887 (mpp) cc_final: 0.5635 (mpp) REVERT: A 275 TYR cc_start: 0.8375 (m-80) cc_final: 0.7961 (m-80) REVERT: A 311 PHE cc_start: 0.9393 (t80) cc_final: 0.9000 (t80) REVERT: A 340 THR cc_start: 0.7826 (p) cc_final: 0.7208 (p) REVERT: A 348 LYS cc_start: 0.9388 (mtmm) cc_final: 0.9008 (mtmm) REVERT: B 264 LEU cc_start: 0.8811 (mm) cc_final: 0.8593 (mm) REVERT: B 275 TYR cc_start: 0.8307 (m-80) cc_final: 0.7965 (m-80) REVERT: B 340 THR cc_start: 0.8218 (p) cc_final: 0.7871 (p) REVERT: D 340 THR cc_start: 0.8101 (p) cc_final: 0.7774 (p) REVERT: E 275 TYR cc_start: 0.8497 (m-80) cc_final: 0.8263 (m-80) REVERT: E 340 THR cc_start: 0.7934 (p) cc_final: 0.7230 (t) REVERT: E 348 LYS cc_start: 0.9378 (mtmm) cc_final: 0.8928 (mtmm) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1358 time to fit residues: 39.9870 Evaluate side-chains 203 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 0.0670 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN D 282 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119846 restraints weight = 8834.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123783 restraints weight = 5675.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126475 restraints weight = 4288.039| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4640 Z= 0.310 Angle : 0.684 6.501 6400 Z= 0.369 Chirality : 0.052 0.225 825 Planarity : 0.006 0.068 795 Dihedral : 6.399 22.305 640 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.32 (0.32), residues: 245 loop : -1.77 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 331 PHE 0.022 0.002 PHE B 314 TYR 0.012 0.001 TYR C 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.535 Fit side-chains REVERT: C 311 PHE cc_start: 0.9218 (t80) cc_final: 0.8717 (t80) REVERT: C 340 THR cc_start: 0.8092 (p) cc_final: 0.7749 (p) REVERT: A 251 PHE cc_start: 0.6644 (p90) cc_final: 0.6341 (p90) REVERT: A 275 TYR cc_start: 0.8393 (m-80) cc_final: 0.8005 (m-80) REVERT: A 311 PHE cc_start: 0.9371 (t80) cc_final: 0.8836 (t80) REVERT: A 340 THR cc_start: 0.7633 (p) cc_final: 0.7178 (p) REVERT: A 348 LYS cc_start: 0.9409 (mtmm) cc_final: 0.9111 (mtmm) REVERT: B 339 LEU cc_start: 0.8487 (mt) cc_final: 0.8230 (mt) REVERT: B 340 THR cc_start: 0.8224 (p) cc_final: 0.7879 (p) REVERT: D 275 TYR cc_start: 0.8802 (m-10) cc_final: 0.8579 (m-10) REVERT: D 300 LYS cc_start: 0.8444 (mtmm) cc_final: 0.8180 (mttm) REVERT: D 340 THR cc_start: 0.8121 (p) cc_final: 0.7779 (p) REVERT: E 339 LEU cc_start: 0.8553 (mt) cc_final: 0.8292 (mt) REVERT: E 340 THR cc_start: 0.7994 (p) cc_final: 0.7322 (t) REVERT: E 348 LYS cc_start: 0.9413 (mtmm) cc_final: 0.9008 (mtmm) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1203 time to fit residues: 35.8089 Evaluate side-chains 196 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 38 optimal weight: 0.0270 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN D 282 GLN E 256 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.172647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117616 restraints weight = 8940.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121512 restraints weight = 5752.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123918 restraints weight = 4360.553| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4640 Z= 0.309 Angle : 0.697 7.592 6400 Z= 0.375 Chirality : 0.052 0.205 825 Planarity : 0.006 0.069 795 Dihedral : 6.497 21.480 640 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.30 (0.32), residues: 245 loop : -1.76 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 331 PHE 0.021 0.002 PHE D 311 TYR 0.013 0.001 TYR E 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: C 340 THR cc_start: 0.8085 (p) cc_final: 0.7784 (p) REVERT: A 251 PHE cc_start: 0.6415 (p90) cc_final: 0.6164 (p90) REVERT: A 275 TYR cc_start: 0.8398 (m-80) cc_final: 0.8012 (m-80) REVERT: A 311 PHE cc_start: 0.9354 (t80) cc_final: 0.8798 (t80) REVERT: A 340 THR cc_start: 0.7491 (p) cc_final: 0.7054 (p) REVERT: B 284 LEU cc_start: 0.9068 (mt) cc_final: 0.8819 (mt) REVERT: B 339 LEU cc_start: 0.8482 (mt) cc_final: 0.8253 (mt) REVERT: B 340 THR cc_start: 0.8160 (p) cc_final: 0.7778 (p) REVERT: D 264 LEU cc_start: 0.8931 (mm) cc_final: 0.8417 (mm) REVERT: D 275 TYR cc_start: 0.8834 (m-10) cc_final: 0.8525 (m-10) REVERT: D 340 THR cc_start: 0.8090 (p) cc_final: 0.7809 (p) REVERT: E 275 TYR cc_start: 0.8777 (m-80) cc_final: 0.8293 (m-80) REVERT: E 339 LEU cc_start: 0.8591 (mt) cc_final: 0.8278 (mt) REVERT: E 340 THR cc_start: 0.7994 (p) cc_final: 0.7279 (t) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1201 time to fit residues: 33.0083 Evaluate side-chains 176 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 256 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.171606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116220 restraints weight = 8885.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120012 restraints weight = 5719.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122864 restraints weight = 4345.263| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4640 Z= 0.342 Angle : 0.706 7.233 6400 Z= 0.382 Chirality : 0.052 0.215 825 Planarity : 0.006 0.069 795 Dihedral : 6.548 22.446 640 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.34 (0.33), residues: 245 loop : -1.76 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 331 PHE 0.021 0.002 PHE D 311 TYR 0.012 0.001 TYR B 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.516 Fit side-chains REVERT: C 340 THR cc_start: 0.7969 (p) cc_final: 0.7607 (p) REVERT: A 251 PHE cc_start: 0.6533 (p90) cc_final: 0.6131 (p90) REVERT: A 264 LEU cc_start: 0.8927 (mm) cc_final: 0.8716 (mm) REVERT: A 275 TYR cc_start: 0.8415 (m-80) cc_final: 0.8057 (m-80) REVERT: A 311 PHE cc_start: 0.9327 (t80) cc_final: 0.8893 (t80) REVERT: A 348 LYS cc_start: 0.9399 (mtmm) cc_final: 0.9083 (mtmm) REVERT: B 339 LEU cc_start: 0.8476 (mt) cc_final: 0.8260 (mt) REVERT: B 340 THR cc_start: 0.8159 (p) cc_final: 0.7783 (p) REVERT: B 348 LYS cc_start: 0.9511 (mtmm) cc_final: 0.9101 (mtmm) REVERT: D 251 PHE cc_start: 0.6625 (p90) cc_final: 0.6381 (p90) REVERT: D 275 TYR cc_start: 0.8912 (m-10) cc_final: 0.8558 (m-10) REVERT: D 340 THR cc_start: 0.8145 (p) cc_final: 0.7844 (p) REVERT: E 275 TYR cc_start: 0.8833 (m-80) cc_final: 0.8558 (m-10) REVERT: E 348 LYS cc_start: 0.9408 (mtmm) cc_final: 0.9020 (mtmm) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1288 time to fit residues: 32.7018 Evaluate side-chains 178 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.0000 chunk 0 optimal weight: 6.9990 overall best weight: 3.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.172348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117287 restraints weight = 8757.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121103 restraints weight = 5654.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123767 restraints weight = 4266.938| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4640 Z= 0.314 Angle : 0.694 7.475 6400 Z= 0.375 Chirality : 0.051 0.260 825 Planarity : 0.006 0.064 795 Dihedral : 6.584 21.693 640 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.30 (0.33), residues: 245 loop : -1.82 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 331 PHE 0.035 0.002 PHE D 311 TYR 0.008 0.001 TYR E 275 =============================================================================== Job complete usr+sys time: 1736.95 seconds wall clock time: 32 minutes 1.71 seconds (1921.71 seconds total)