Starting phenix.real_space_refine on Thu Mar 6 02:00:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cz6_30507/03_2025/7cz6_30507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cz6_30507/03_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_30507/03_2025/7cz6_30507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cz6_30507/03_2025/7cz6_30507.map" model { file = "/net/cci-nas-00/data/ceres_data/7cz6_30507/03_2025/7cz6_30507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cz6_30507/03_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-5624/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: 2.23, per 1000 atoms: 0.49 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: 1.32 Conformation dependent library (CDL) restraints added in 661.6 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: 0.59 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: 1.15 Time building geometry restraints manager: 1.52 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: 0.060 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.060 Find NCS groups from input model: 0.110 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- 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 : 0.522 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: 0.1216 time to fit residues: 38.9953 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 : 0.505 ------------------------------------------------------------------------------- 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: 3.9990 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: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.171623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124513 restraints weight = 8722.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128830 restraints weight = 5342.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131711 restraints weight = 3821.245| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4640 Z= 0.341 Angle : 0.800 8.150 6400 Z= 0.440 Chirality : 0.052 0.154 825 Planarity : 0.007 0.056 795 Dihedral : 7.840 25.751 640 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % 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: -1.01 (0.34), residues: 245 loop : -1.63 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 331 PHE 0.025 0.003 PHE D 307 TYR 0.015 0.003 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 231 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 275 TYR cc_start: 0.8522 (m-80) cc_final: 0.8137 (m-80) REVERT: C 276 GLN cc_start: 0.8401 (tt0) cc_final: 0.7379 (tt0) REVERT: C 284 LEU cc_start: 0.9281 (mt) cc_final: 0.8995 (mt) REVERT: C 311 PHE cc_start: 0.9205 (t80) cc_final: 0.8852 (t80) REVERT: C 318 THR cc_start: 0.8767 (p) cc_final: 0.8524 (p) REVERT: A 275 TYR cc_start: 0.8487 (m-80) cc_final: 0.8154 (m-80) REVERT: A 284 LEU cc_start: 0.9189 (mt) cc_final: 0.8876 (mt) REVERT: A 311 PHE cc_start: 0.9302 (t80) cc_final: 0.8999 (t80) REVERT: B 262 GLN cc_start: 0.8343 (pp30) cc_final: 0.7664 (pp30) REVERT: B 264 LEU cc_start: 0.9052 (pp) cc_final: 0.8712 (mm) REVERT: B 275 TYR cc_start: 0.8430 (m-80) cc_final: 0.7928 (m-80) REVERT: B 311 PHE cc_start: 0.9314 (t80) cc_final: 0.8884 (t80) REVERT: B 340 THR cc_start: 0.7787 (p) cc_final: 0.7414 (p) REVERT: D 275 TYR cc_start: 0.8415 (m-80) cc_final: 0.8052 (m-80) REVERT: D 284 LEU cc_start: 0.9008 (mt) cc_final: 0.8770 (mt) REVERT: D 339 LEU cc_start: 0.8385 (mt) cc_final: 0.8154 (mt) REVERT: D 340 THR cc_start: 0.7654 (p) cc_final: 0.7244 (p) REVERT: E 275 TYR cc_start: 0.8431 (m-80) cc_final: 0.8053 (m-80) REVERT: E 340 THR cc_start: 0.7691 (p) cc_final: 0.7337 (p) outliers start: 1 outliers final: 1 residues processed: 230 average time/residue: 0.1224 time to fit residues: 36.9942 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 : 0.532 ------------------------------------------------------------------------------- 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: 10.0000 chunk 47 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 305 GLN A 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.168274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.117682 restraints weight = 9111.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121285 restraints weight = 5747.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124076 restraints weight = 4323.578| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4640 Z= 0.300 Angle : 0.712 7.050 6400 Z= 0.388 Chirality : 0.049 0.180 825 Planarity : 0.006 0.064 795 Dihedral : 6.954 20.194 640 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -1.98 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.71 (0.36), residues: 245 loop : -1.78 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 331 PHE 0.017 0.002 PHE D 311 TYR 0.010 0.001 TYR B 275 *********************** 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 : 0.511 Fit side-chains REVERT: C 275 TYR cc_start: 0.8443 (m-80) cc_final: 0.7740 (m-80) REVERT: C 308 ASP cc_start: 0.9074 (m-30) cc_final: 0.8846 (m-30) REVERT: C 311 PHE cc_start: 0.9252 (t80) cc_final: 0.8872 (t80) REVERT: C 318 THR cc_start: 0.9011 (p) cc_final: 0.8772 (p) REVERT: C 340 THR cc_start: 0.7873 (p) cc_final: 0.7560 (p) REVERT: A 275 TYR cc_start: 0.8292 (m-80) cc_final: 0.7491 (m-80) REVERT: A 308 ASP cc_start: 0.9158 (m-30) cc_final: 0.8949 (m-30) REVERT: A 311 PHE cc_start: 0.9397 (t80) cc_final: 0.9034 (t80) REVERT: A 339 LEU cc_start: 0.8449 (mt) cc_final: 0.8171 (mt) REVERT: B 308 ASP cc_start: 0.8975 (m-30) cc_final: 0.8740 (m-30) REVERT: B 311 PHE cc_start: 0.9176 (t80) cc_final: 0.8901 (t80) REVERT: B 339 LEU cc_start: 0.8520 (mt) cc_final: 0.8113 (mt) REVERT: B 340 THR cc_start: 0.8013 (p) cc_final: 0.7673 (p) REVERT: D 329 VAL cc_start: 0.9529 (t) cc_final: 0.9237 (t) REVERT: D 340 THR cc_start: 0.7865 (p) cc_final: 0.7520 (p) REVERT: E 308 ASP cc_start: 0.9063 (m-30) cc_final: 0.8755 (m-30) REVERT: E 318 THR cc_start: 0.8927 (p) cc_final: 0.8663 (p) REVERT: E 339 LEU cc_start: 0.8470 (mt) cc_final: 0.8238 (mt) REVERT: E 340 THR cc_start: 0.7919 (p) cc_final: 0.7278 (t) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1207 time to fit residues: 35.9872 Evaluate side-chains 197 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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: 3.9990 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 30.0000 chunk 59 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** 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 = 0.4092 r_free = 0.4092 target = 0.172304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120109 restraints weight = 8948.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123956 restraints weight = 5615.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126757 restraints weight = 4176.790| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4640 Z= 0.237 Angle : 0.666 7.313 6400 Z= 0.360 Chirality : 0.049 0.158 825 Planarity : 0.006 0.067 795 Dihedral : 6.556 21.098 640 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -1.94 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.75 (0.35), residues: 245 loop : -1.70 (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 0.019 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 230 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.541 Fit side-chains REVERT: C 275 TYR cc_start: 0.8402 (m-80) cc_final: 0.7952 (m-80) REVERT: C 276 GLN cc_start: 0.8915 (tt0) cc_final: 0.8571 (pt0) REVERT: C 308 ASP cc_start: 0.8964 (m-30) cc_final: 0.8756 (m-30) REVERT: C 311 PHE cc_start: 0.9243 (t80) cc_final: 0.8851 (t80) REVERT: C 340 THR cc_start: 0.7702 (p) cc_final: 0.7351 (p) REVERT: A 275 TYR cc_start: 0.8226 (m-80) cc_final: 0.7531 (m-80) REVERT: A 311 PHE cc_start: 0.9394 (t80) cc_final: 0.9046 (t80) REVERT: A 339 LEU cc_start: 0.8469 (mt) cc_final: 0.8191 (mt) REVERT: B 275 TYR cc_start: 0.8119 (m-80) cc_final: 0.7506 (m-80) REVERT: B 308 ASP cc_start: 0.9042 (m-30) cc_final: 0.8825 (m-30) REVERT: B 311 PHE cc_start: 0.9171 (t80) cc_final: 0.8827 (t80) REVERT: B 340 THR cc_start: 0.8085 (p) cc_final: 0.7685 (p) REVERT: D 314 PHE cc_start: 0.8291 (m-80) cc_final: 0.7965 (m-10) REVERT: D 340 THR cc_start: 0.8021 (p) cc_final: 0.7699 (p) REVERT: E 264 LEU cc_start: 0.8919 (mm) cc_final: 0.8623 (mm) REVERT: E 275 TYR cc_start: 0.8429 (m-80) cc_final: 0.7862 (m-80) REVERT: E 308 ASP cc_start: 0.9061 (m-30) cc_final: 0.8731 (m-30) REVERT: E 340 THR cc_start: 0.8160 (p) cc_final: 0.7831 (p) REVERT: E 348 LYS cc_start: 0.9362 (mtmm) cc_final: 0.8704 (mtmm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1175 time to fit residues: 36.4127 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 : 0.698 ------------------------------------------------------------------------------- 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: 10.0000 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 43 optimal weight: 0.0970 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 253 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.174899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122424 restraints weight = 8651.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126380 restraints weight = 5397.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129375 restraints weight = 4009.020| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4640 Z= 0.268 Angle : 0.685 6.630 6400 Z= 0.367 Chirality : 0.049 0.159 825 Planarity : 0.006 0.066 795 Dihedral : 6.485 21.854 640 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.19 % Allowed : 1.73 % 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: -1.87 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.63 (0.34), residues: 245 loop : -1.73 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 331 PHE 0.032 0.002 PHE B 314 TYR 0.019 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 227 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: C 275 TYR cc_start: 0.8409 (m-80) cc_final: 0.8070 (m-80) REVERT: C 311 PHE cc_start: 0.9223 (t80) cc_final: 0.8785 (t80) REVERT: C 340 THR cc_start: 0.7728 (p) cc_final: 0.7371 (p) REVERT: A 251 PHE cc_start: 0.6595 (p90) cc_final: 0.6394 (p90) REVERT: A 275 TYR cc_start: 0.8285 (m-80) cc_final: 0.7753 (m-80) REVERT: A 311 PHE cc_start: 0.9421 (t80) cc_final: 0.9053 (t80) REVERT: A 340 THR cc_start: 0.7838 (p) cc_final: 0.7450 (p) REVERT: A 348 LYS cc_start: 0.9357 (mtmm) cc_final: 0.8961 (mtmm) REVERT: B 275 TYR cc_start: 0.8273 (m-80) cc_final: 0.7785 (m-80) REVERT: B 308 ASP cc_start: 0.9058 (m-30) cc_final: 0.8789 (m-30) REVERT: B 311 PHE cc_start: 0.9226 (t80) cc_final: 0.8832 (t80) REVERT: B 340 THR cc_start: 0.8106 (p) cc_final: 0.7696 (p) REVERT: D 262 GLN cc_start: 0.7013 (tp40) cc_final: 0.6620 (tp40) REVERT: D 340 THR cc_start: 0.8216 (p) cc_final: 0.7854 (p) REVERT: E 275 TYR cc_start: 0.8351 (m-80) cc_final: 0.7839 (m-80) REVERT: E 308 ASP cc_start: 0.8946 (m-30) cc_final: 0.8656 (m-30) REVERT: E 339 LEU cc_start: 0.8483 (mt) cc_final: 0.8282 (mt) REVERT: E 340 THR cc_start: 0.8080 (p) cc_final: 0.7736 (p) outliers start: 1 outliers final: 1 residues processed: 227 average time/residue: 0.1156 time to fit residues: 35.3184 Evaluate side-chains 210 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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: 20.0000 chunk 49 optimal weight: 0.0170 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN B 253 ASN 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 = 0.4084 r_free = 0.4084 target = 0.172088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117888 restraints weight = 8807.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121805 restraints weight = 5653.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124362 restraints weight = 4259.988| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4640 Z= 0.290 Angle : 0.669 6.149 6400 Z= 0.362 Chirality : 0.049 0.151 825 Planarity : 0.006 0.070 795 Dihedral : 6.471 21.583 640 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.19 % Allowed : 1.73 % 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: -1.86 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.52 (0.34), residues: 245 loop : -1.80 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 331 PHE 0.026 0.002 PHE B 314 TYR 0.013 0.002 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 227 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: C 311 PHE cc_start: 0.9268 (t80) cc_final: 0.8890 (t80) REVERT: C 314 PHE cc_start: 0.7891 (m-80) cc_final: 0.7463 (m-10) REVERT: C 340 THR cc_start: 0.7760 (p) cc_final: 0.7390 (p) REVERT: A 275 TYR cc_start: 0.8311 (m-80) cc_final: 0.7873 (m-80) REVERT: A 311 PHE cc_start: 0.9424 (t80) cc_final: 0.9021 (t80) REVERT: A 340 THR cc_start: 0.7777 (p) cc_final: 0.7414 (p) REVERT: A 348 LYS cc_start: 0.9403 (mtmm) cc_final: 0.9014 (mtmm) REVERT: B 264 LEU cc_start: 0.8823 (mm) cc_final: 0.8597 (mm) REVERT: B 275 TYR cc_start: 0.8339 (m-80) cc_final: 0.7951 (m-80) REVERT: B 311 PHE cc_start: 0.9280 (t80) cc_final: 0.8988 (t80) REVERT: B 340 THR cc_start: 0.8482 (p) cc_final: 0.8163 (p) REVERT: B 348 LYS cc_start: 0.9519 (mtmm) cc_final: 0.9235 (mtmm) REVERT: D 340 THR cc_start: 0.8134 (p) cc_final: 0.7766 (p) REVERT: E 275 TYR cc_start: 0.8416 (m-80) cc_final: 0.8060 (m-80) REVERT: E 308 ASP cc_start: 0.8935 (m-30) cc_final: 0.8704 (m-30) REVERT: E 340 THR cc_start: 0.8157 (p) cc_final: 0.7754 (p) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1130 time to fit residues: 34.4070 Evaluate side-chains 210 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 31 optimal weight: 0.0050 chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 253 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN ** 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 = 0.4140 r_free = 0.4140 target = 0.176068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122960 restraints weight = 8686.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127159 restraints weight = 5533.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129495 restraints weight = 4133.759| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4640 Z= 0.213 Angle : 0.662 8.013 6400 Z= 0.351 Chirality : 0.050 0.169 825 Planarity : 0.006 0.063 795 Dihedral : 6.200 20.557 640 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % 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: -1.71 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.37 (0.33), residues: 245 loop : -1.74 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 331 PHE 0.020 0.002 PHE E 311 TYR 0.012 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 225 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: C 275 TYR cc_start: 0.8762 (m-80) cc_final: 0.8533 (m-10) REVERT: C 311 PHE cc_start: 0.9251 (t80) cc_final: 0.8725 (t80) REVERT: C 314 PHE cc_start: 0.7929 (m-80) cc_final: 0.7539 (m-10) REVERT: C 340 THR cc_start: 0.8179 (p) cc_final: 0.7871 (p) REVERT: A 251 PHE cc_start: 0.6226 (p90) cc_final: 0.6011 (p90) REVERT: A 275 TYR cc_start: 0.8363 (m-80) cc_final: 0.7978 (m-80) REVERT: A 311 PHE cc_start: 0.9432 (t80) cc_final: 0.9018 (t80) REVERT: A 339 LEU cc_start: 0.8648 (mt) cc_final: 0.8300 (mt) REVERT: A 340 THR cc_start: 0.7792 (p) cc_final: 0.7379 (p) REVERT: B 275 TYR cc_start: 0.8266 (m-80) cc_final: 0.7944 (m-80) REVERT: B 311 PHE cc_start: 0.9281 (t80) cc_final: 0.9010 (t80) REVERT: B 340 THR cc_start: 0.8347 (p) cc_final: 0.7999 (p) REVERT: B 348 LYS cc_start: 0.9477 (mtmm) cc_final: 0.9138 (mtmm) REVERT: D 340 THR cc_start: 0.8096 (p) cc_final: 0.7756 (p) REVERT: E 275 TYR cc_start: 0.8523 (m-80) cc_final: 0.8282 (m-80) REVERT: E 308 ASP cc_start: 0.8901 (m-30) cc_final: 0.8677 (m-30) REVERT: E 314 PHE cc_start: 0.8072 (m-80) cc_final: 0.7837 (m-10) REVERT: E 340 THR cc_start: 0.8047 (p) cc_final: 0.7745 (p) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1375 time to fit residues: 41.1257 Evaluate side-chains 202 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 7.9990 chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- 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** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 256 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.169476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115594 restraints weight = 9036.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119434 restraints weight = 5669.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122157 restraints weight = 4272.958| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 4640 Z= 0.458 Angle : 0.744 6.170 6400 Z= 0.407 Chirality : 0.052 0.284 825 Planarity : 0.007 0.072 795 Dihedral : 6.765 22.422 640 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % 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: -1.90 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.34 (0.33), residues: 245 loop : -1.99 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 331 PHE 0.021 0.002 PHE D 311 TYR 0.017 0.002 TYR D 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 205 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: C 264 LEU cc_start: 0.8955 (mm) cc_final: 0.8647 (mm) REVERT: C 275 TYR cc_start: 0.8887 (m-80) cc_final: 0.8528 (m-10) REVERT: C 308 ASP cc_start: 0.8942 (m-30) cc_final: 0.8729 (m-30) REVERT: C 340 THR cc_start: 0.8142 (p) cc_final: 0.7792 (p) REVERT: A 275 TYR cc_start: 0.8373 (m-80) cc_final: 0.8017 (m-80) REVERT: A 311 PHE cc_start: 0.9460 (t80) cc_final: 0.8997 (t80) REVERT: A 339 LEU cc_start: 0.8782 (mt) cc_final: 0.8469 (mt) REVERT: A 340 THR cc_start: 0.7834 (p) cc_final: 0.7345 (p) REVERT: B 284 LEU cc_start: 0.9109 (mt) cc_final: 0.8815 (mt) REVERT: B 311 PHE cc_start: 0.9326 (t80) cc_final: 0.8972 (t80) REVERT: B 339 LEU cc_start: 0.8522 (mt) cc_final: 0.8258 (mt) REVERT: B 340 THR cc_start: 0.8353 (p) cc_final: 0.7979 (p) REVERT: D 264 LEU cc_start: 0.8966 (mm) cc_final: 0.8764 (mm) REVERT: D 275 TYR cc_start: 0.8834 (m-10) cc_final: 0.8496 (m-10) REVERT: D 340 THR cc_start: 0.8194 (p) cc_final: 0.7856 (p) REVERT: E 308 ASP cc_start: 0.8942 (m-30) cc_final: 0.8726 (m-30) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1747 time to fit residues: 46.9427 Evaluate side-chains 163 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 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** D 282 GLN E 256 ASN E 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.173823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118794 restraints weight = 8693.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122851 restraints weight = 5538.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125689 restraints weight = 4180.754| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4640 Z= 0.255 Angle : 0.703 9.869 6400 Z= 0.375 Chirality : 0.052 0.204 825 Planarity : 0.006 0.063 795 Dihedral : 6.549 21.743 640 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -1.80 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.35 (0.33), residues: 245 loop : -1.86 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 331 PHE 0.024 0.002 PHE D 297 TYR 0.019 0.001 TYR D 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 214 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: C 275 TYR cc_start: 0.8903 (m-80) cc_final: 0.8496 (m-10) REVERT: C 340 THR cc_start: 0.8057 (p) cc_final: 0.7757 (p) REVERT: A 251 PHE cc_start: 0.6429 (p90) cc_final: 0.6046 (p90) REVERT: A 275 TYR cc_start: 0.8457 (m-80) cc_final: 0.8128 (m-80) REVERT: A 311 PHE cc_start: 0.9453 (t80) cc_final: 0.8997 (t80) REVERT: A 339 LEU cc_start: 0.8741 (mt) cc_final: 0.8463 (mt) REVERT: A 340 THR cc_start: 0.7785 (p) cc_final: 0.7425 (p) REVERT: A 348 LYS cc_start: 0.9428 (mtmm) cc_final: 0.9137 (mtmm) REVERT: B 339 LEU cc_start: 0.8521 (mt) cc_final: 0.8199 (mt) REVERT: B 340 THR cc_start: 0.8322 (p) cc_final: 0.8003 (p) REVERT: B 348 LYS cc_start: 0.9458 (mtmm) cc_final: 0.9206 (mtmm) REVERT: D 251 PHE cc_start: 0.6409 (p90) cc_final: 0.6136 (p90) REVERT: D 264 LEU cc_start: 0.8819 (mm) cc_final: 0.8539 (mm) REVERT: D 275 TYR cc_start: 0.8882 (m-10) cc_final: 0.8530 (m-10) REVERT: D 340 THR cc_start: 0.8157 (p) cc_final: 0.7869 (p) REVERT: E 275 TYR cc_start: 0.8728 (m-80) cc_final: 0.8521 (m-80) REVERT: E 308 ASP cc_start: 0.8962 (m-30) cc_final: 0.8754 (m-30) REVERT: E 339 LEU cc_start: 0.8711 (mt) cc_final: 0.8505 (mt) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1663 time to fit residues: 48.2414 Evaluate side-chains 183 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 1.9990 chunk 35 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 282 GLN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 256 ASN ** E 262 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 = 0.4103 r_free = 0.4103 target = 0.172875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118792 restraints weight = 8738.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122786 restraints weight = 5545.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125393 restraints weight = 4161.212| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4640 Z= 0.298 Angle : 0.695 8.466 6400 Z= 0.375 Chirality : 0.052 0.200 825 Planarity : 0.006 0.062 795 Dihedral : 6.639 22.651 640 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.70 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: -1.79 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.36 (0.33), residues: 245 loop : -1.85 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 331 PHE 0.039 0.003 PHE B 314 TYR 0.015 0.001 TYR D 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 208 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: C 275 TYR cc_start: 0.8924 (m-80) cc_final: 0.8522 (m-10) REVERT: C 340 THR cc_start: 0.8100 (p) cc_final: 0.7792 (p) REVERT: A 275 TYR cc_start: 0.8466 (m-80) cc_final: 0.8146 (m-80) REVERT: A 308 ASP cc_start: 0.8990 (m-30) cc_final: 0.8770 (m-30) REVERT: A 311 PHE cc_start: 0.9426 (t80) cc_final: 0.8855 (t80) REVERT: A 339 LEU cc_start: 0.8760 (mt) cc_final: 0.8473 (mt) REVERT: A 340 THR cc_start: 0.7811 (p) cc_final: 0.7430 (p) REVERT: B 340 THR cc_start: 0.8306 (p) cc_final: 0.7948 (p) REVERT: B 348 LYS cc_start: 0.9501 (mtmm) cc_final: 0.9073 (mtmm) REVERT: D 251 PHE cc_start: 0.6376 (p90) cc_final: 0.6035 (p90) REVERT: D 274 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7523 (ttmt) REVERT: D 275 TYR cc_start: 0.8888 (m-10) cc_final: 0.8499 (m-10) REVERT: D 340 THR cc_start: 0.8237 (p) cc_final: 0.7932 (p) REVERT: E 275 TYR cc_start: 0.8693 (m-80) cc_final: 0.8416 (m-80) REVERT: E 311 PHE cc_start: 0.8968 (t80) cc_final: 0.8764 (t80) REVERT: E 339 LEU cc_start: 0.8727 (mt) cc_final: 0.8516 (mt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2146 time to fit residues: 60.5399 Evaluate side-chains 181 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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: 0.0050 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 23 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.4176 ------------------------------------------------------------------------------- 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 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.169877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119934 restraints weight = 8786.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123523 restraints weight = 5643.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125989 restraints weight = 4273.859| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4640 Z= 0.258 Angle : 0.694 8.886 6400 Z= 0.367 Chirality : 0.052 0.197 825 Planarity : 0.006 0.059 795 Dihedral : 6.516 23.630 640 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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: -1.81 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.37 (0.33), residues: 245 loop : -1.85 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 331 PHE 0.045 0.003 PHE D 311 TYR 0.015 0.001 TYR D 275 =============================================================================== Job complete usr+sys time: 2118.15 seconds wall clock time: 39 minutes 27.42 seconds (2367.42 seconds total)