Starting phenix.real_space_refine on Tue Jan 14 03:56:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxb_18717/01_2025/8qxb_18717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxb_18717/01_2025/8qxb_18717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qxb_18717/01_2025/8qxb_18717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxb_18717/01_2025/8qxb_18717.map" model { file = "/net/cci-nas-00/data/ceres_data/8qxb_18717/01_2025/8qxb_18717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxb_18717/01_2025/8qxb_18717.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 126 5.16 5 C 3348 2.51 5 N 990 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5544 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R Time building chain proxies: 1.94, per 1000 atoms: 0.35 Number of scatterers: 5544 At special positions: 0 Unit cell: (109.2, 104, 46.8, 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 126 16.00 O 1080 8.00 N 990 7.00 C 3348 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: 1.30 Conformation dependent library (CDL) restraints added in 714.5 milliseconds 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.021A pdb=" N SER A 317 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER D 317 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER G 317 " --> pdb=" O ILE J 318 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER J 317 " --> pdb=" O ILE M 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER M 317 " --> pdb=" O ILE P 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 331 removed outlier: 5.905A pdb=" N ALA A 328 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN D 331 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A 330 " --> pdb=" O GLN D 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA D 328 " --> pdb=" O ALA G 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN G 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 330 " --> pdb=" O GLN G 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA G 328 " --> pdb=" O ALA J 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN J 331 " --> pdb=" O ALA G 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU G 330 " --> pdb=" O GLN J 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA J 328 " --> pdb=" O ALA M 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN M 331 " --> pdb=" O ALA J 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU J 330 " --> pdb=" O GLN M 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA M 328 " --> pdb=" O ALA P 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN P 331 " --> pdb=" O ALA M 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU M 330 " --> pdb=" O GLN P 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 318 removed outlier: 6.022A pdb=" N SER B 317 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER E 317 " --> pdb=" O ILE H 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER H 317 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER K 317 " --> pdb=" O ILE N 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER N 317 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 331 removed outlier: 5.905A pdb=" N ALA B 328 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN E 331 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU B 330 " --> pdb=" O GLN E 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA E 328 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN H 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU E 330 " --> pdb=" O GLN H 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA H 328 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN K 331 " --> pdb=" O ALA H 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU H 330 " --> pdb=" O GLN K 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA K 328 " --> pdb=" O ALA N 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN N 331 " --> pdb=" O ALA K 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU K 330 " --> pdb=" O GLN N 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA N 328 " --> pdb=" O ALA Q 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN Q 331 " --> pdb=" O ALA N 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU N 330 " --> pdb=" O GLN Q 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.022A pdb=" N SER C 317 " --> pdb=" O ILE F 318 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER F 317 " --> pdb=" O ILE I 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER I 317 " --> pdb=" O ILE L 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER L 317 " --> pdb=" O ILE O 318 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER O 317 " --> pdb=" O ILE R 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 331 removed outlier: 5.905A pdb=" N ALA C 328 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN F 331 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU C 330 " --> pdb=" O GLN F 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA F 328 " --> pdb=" O ALA I 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN I 331 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU F 330 " --> pdb=" O GLN I 331 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA I 328 " --> pdb=" O ALA L 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN L 331 " --> pdb=" O ALA I 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU I 330 " --> pdb=" O GLN L 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA L 328 " --> pdb=" O ALA O 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN O 331 " --> pdb=" O ALA L 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU L 330 " --> pdb=" O GLN O 331 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA O 328 " --> pdb=" O ALA R 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN R 331 " --> pdb=" O ALA O 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU O 330 " --> pdb=" O GLN R 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.16 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 990 1.32 - 1.44: 1440 1.44 - 1.57: 2934 1.57 - 1.69: 0 1.69 - 1.82: 252 Bond restraints: 5616 Sorted by residual: bond pdb=" C SER J 317 " pdb=" O SER J 317 " ideal model delta sigma weight residual 1.235 1.193 0.043 1.13e-02 7.83e+03 1.41e+01 bond pdb=" C SER C 317 " pdb=" O SER C 317 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.13e-02 7.83e+03 1.41e+01 bond pdb=" C SER A 317 " pdb=" O SER A 317 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.13e-02 7.83e+03 1.41e+01 bond pdb=" C SER M 317 " pdb=" O SER M 317 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.13e-02 7.83e+03 1.41e+01 bond pdb=" C SER D 317 " pdb=" O SER D 317 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.13e-02 7.83e+03 1.41e+01 ... (remaining 5611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 3956 1.33 - 2.66: 1559 2.66 - 3.99: 1205 3.99 - 5.32: 601 5.32 - 6.66: 149 Bond angle restraints: 7470 Sorted by residual: angle pdb=" N GLN O 327 " pdb=" CA GLN O 327 " pdb=" C GLN O 327 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.32e+01 angle pdb=" N GLN H 327 " pdb=" CA GLN H 327 " pdb=" C GLN H 327 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.31e+01 angle pdb=" N GLN N 327 " pdb=" CA GLN N 327 " pdb=" C GLN N 327 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.31e+01 angle pdb=" N GLN J 327 " pdb=" CA GLN J 327 " pdb=" C GLN J 327 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.31e+01 angle pdb=" N GLN G 327 " pdb=" CA GLN G 327 " pdb=" C GLN G 327 " ideal model delta sigma weight residual 111.07 104.92 6.15 1.07e+00 8.73e-01 3.30e+01 ... (remaining 7465 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 15.30: 2880 15.30 - 30.56: 234 30.56 - 45.83: 108 45.83 - 61.10: 36 61.10 - 76.36: 36 Dihedral angle restraints: 3294 sinusoidal: 1170 harmonic: 2124 Sorted by residual: dihedral pdb=" C PHE L 316 " pdb=" N PHE L 316 " pdb=" CA PHE L 316 " pdb=" CB PHE L 316 " ideal model delta harmonic sigma weight residual -122.60 -114.29 -8.31 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C PHE F 316 " pdb=" N PHE F 316 " pdb=" CA PHE F 316 " pdb=" CB PHE F 316 " ideal model delta harmonic sigma weight residual -122.60 -114.29 -8.31 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C PHE K 316 " pdb=" N PHE K 316 " pdb=" CA PHE K 316 " pdb=" CB PHE K 316 " ideal model delta harmonic sigma weight residual -122.60 -114.30 -8.30 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 3291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 242 0.053 - 0.106: 208 0.106 - 0.160: 162 0.160 - 0.213: 54 0.213 - 0.266: 54 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA TRP G 334 " pdb=" N TRP G 334 " pdb=" C TRP G 334 " pdb=" CB TRP G 334 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA TRP M 334 " pdb=" N TRP M 334 " pdb=" C TRP M 334 " pdb=" CB TRP M 334 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA TRP D 334 " pdb=" N TRP D 334 " pdb=" C TRP D 334 " pdb=" CB TRP D 334 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.76e+00 ... (remaining 717 not shown) Planarity restraints: 1026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO Q 320 " 0.014 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C PRO Q 320 " -0.052 2.00e-02 2.50e+03 pdb=" O PRO Q 320 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA Q 321 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 320 " 0.014 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C PRO H 320 " -0.052 2.00e-02 2.50e+03 pdb=" O PRO H 320 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA H 321 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO M 320 " -0.014 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C PRO M 320 " 0.052 2.00e-02 2.50e+03 pdb=" O PRO M 320 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA M 321 " -0.018 2.00e-02 2.50e+03 ... (remaining 1023 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2559 2.99 - 3.47: 5265 3.47 - 3.94: 9271 3.94 - 4.42: 10560 4.42 - 4.90: 20365 Nonbonded interactions: 48020 Sorted by model distance: nonbonded pdb=" N PRO B 320 " pdb=" O PRO B 320 " model vdw 2.508 2.496 nonbonded pdb=" N PRO A 320 " pdb=" O PRO A 320 " model vdw 2.509 2.496 nonbonded pdb=" N PRO P 320 " pdb=" O PRO P 320 " model vdw 2.509 2.496 nonbonded pdb=" N PRO C 320 " pdb=" O PRO C 320 " model vdw 2.509 2.496 nonbonded pdb=" N PRO H 320 " pdb=" O PRO H 320 " model vdw 2.509 2.496 ... (remaining 48015 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'R' } 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: 0.730 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.350 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 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 : 0.014 0.046 5616 Z= 1.055 Angle : 2.276 6.656 7470 Z= 1.679 Chirality : 0.115 0.266 720 Planarity : 0.010 0.030 1026 Dihedral : 18.192 76.362 1962 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.18), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.14), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.010 TRP O 334 PHE 0.006 0.003 PHE Q 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8052 (ttt) cc_final: 0.7843 (ttp) REVERT: A 323 MET cc_start: 0.6862 (ttm) cc_final: 0.6644 (ttt) REVERT: A 334 TRP cc_start: 0.6777 (p90) cc_final: 0.5394 (m100) REVERT: B 307 MET cc_start: 0.8224 (ttt) cc_final: 0.7898 (ttp) REVERT: B 334 TRP cc_start: 0.6702 (p90) cc_final: 0.5018 (m100) REVERT: C 334 TRP cc_start: 0.6713 (p90) cc_final: 0.4824 (m100) REVERT: E 305 SER cc_start: 0.6314 (m) cc_final: 0.6104 (m) REVERT: E 307 MET cc_start: 0.8478 (ttt) cc_final: 0.8100 (ttt) REVERT: F 307 MET cc_start: 0.8411 (ttt) cc_final: 0.8168 (ttt) REVERT: F 334 TRP cc_start: 0.6975 (p90) cc_final: 0.6749 (p90) REVERT: H 307 MET cc_start: 0.8441 (ttt) cc_final: 0.8208 (ttm) REVERT: I 305 SER cc_start: 0.6337 (m) cc_final: 0.6030 (m) REVERT: K 305 SER cc_start: 0.6294 (m) cc_final: 0.6076 (m) REVERT: L 307 MET cc_start: 0.8216 (ttt) cc_final: 0.7777 (ttt) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1352 time to fit residues: 58.4425 Evaluate side-chains 227 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 327 GLN C 327 GLN E 343 GLN G 343 GLN ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN I 343 GLN I 344 GLN ** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 343 GLN O 343 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.251021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.157224 restraints weight = 7558.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.162415 restraints weight = 4084.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.165489 restraints weight = 2791.825| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5616 Z= 0.149 Angle : 0.695 7.017 7470 Z= 0.351 Chirality : 0.039 0.116 720 Planarity : 0.003 0.030 1026 Dihedral : 5.427 14.674 792 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.68 % Allowed : 41.95 % Favored : 55.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.20), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.15), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 334 PHE 0.007 0.001 PHE L 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 0.625 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: A 323 MET cc_start: 0.7297 (ttm) cc_final: 0.6669 (ttt) REVERT: B 339 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7683 (ptp) REVERT: B 340 LEU cc_start: 0.8478 (tt) cc_final: 0.8211 (tt) REVERT: C 340 LEU cc_start: 0.8373 (tt) cc_final: 0.8138 (tt) REVERT: D 322 MET cc_start: 0.7207 (mmm) cc_final: 0.6677 (mmt) REVERT: D 327 GLN cc_start: 0.8888 (tp40) cc_final: 0.7973 (tm-30) REVERT: D 336 MET cc_start: 0.7818 (ttp) cc_final: 0.7360 (ttt) REVERT: D 339 MET cc_start: 0.8391 (ptm) cc_final: 0.7797 (ptp) REVERT: D 340 LEU cc_start: 0.8306 (tt) cc_final: 0.8024 (tt) REVERT: E 322 MET cc_start: 0.6857 (mmm) cc_final: 0.4095 (ptp) REVERT: E 327 GLN cc_start: 0.8872 (tp40) cc_final: 0.7956 (tm-30) REVERT: F 327 GLN cc_start: 0.8788 (tp40) cc_final: 0.7685 (tp40) REVERT: F 339 MET cc_start: 0.8089 (ttp) cc_final: 0.7569 (mtt) REVERT: F 346 GLN cc_start: 0.8826 (mt0) cc_final: 0.7974 (tt0) REVERT: G 311 MET cc_start: 0.8323 (ptp) cc_final: 0.7853 (ptp) REVERT: G 327 GLN cc_start: 0.8832 (tp40) cc_final: 0.8038 (tm-30) REVERT: H 327 GLN cc_start: 0.8758 (tp40) cc_final: 0.8005 (tm-30) REVERT: I 305 SER cc_start: 0.7781 (m) cc_final: 0.7511 (p) REVERT: I 311 MET cc_start: 0.8550 (ptp) cc_final: 0.8326 (ptp) REVERT: J 327 GLN cc_start: 0.8606 (tp40) cc_final: 0.7840 (tm-30) REVERT: K 327 GLN cc_start: 0.8687 (tp40) cc_final: 0.7846 (tm-30) REVERT: K 334 TRP cc_start: 0.7763 (p90) cc_final: 0.7206 (p90) REVERT: L 322 MET cc_start: 0.6994 (mmt) cc_final: 0.6150 (mmt) REVERT: L 327 GLN cc_start: 0.8496 (tp40) cc_final: 0.8003 (tm-30) REVERT: M 327 GLN cc_start: 0.8553 (tp40) cc_final: 0.7992 (tp40) REVERT: M 334 TRP cc_start: 0.8114 (p90) cc_final: 0.7875 (p90) REVERT: M 336 MET cc_start: 0.7286 (ttp) cc_final: 0.6362 (ttp) REVERT: N 327 GLN cc_start: 0.8844 (tp40) cc_final: 0.8129 (tm-30) REVERT: N 339 MET cc_start: 0.8311 (ptm) cc_final: 0.7793 (ptp) REVERT: O 311 MET cc_start: 0.8322 (ptp) cc_final: 0.7967 (ptp) REVERT: O 322 MET cc_start: 0.7034 (mmm) cc_final: 0.5715 (mmt) REVERT: O 327 GLN cc_start: 0.8821 (tp40) cc_final: 0.8462 (tm-30) REVERT: O 334 TRP cc_start: 0.7884 (p90) cc_final: 0.7456 (p90) REVERT: O 339 MET cc_start: 0.8862 (ptp) cc_final: 0.8632 (ptp) REVERT: P 311 MET cc_start: 0.8539 (ptp) cc_final: 0.8106 (ptp) REVERT: P 336 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6931 (ttt) REVERT: Q 313 PHE cc_start: 0.8155 (m-10) cc_final: 0.7953 (m-10) REVERT: Q 337 MET cc_start: 0.7194 (mmt) cc_final: 0.6762 (mtt) REVERT: Q 339 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7628 (tpt) REVERT: R 311 MET cc_start: 0.8555 (ptp) cc_final: 0.8332 (ptp) REVERT: R 313 PHE cc_start: 0.8224 (m-10) cc_final: 0.7990 (m-10) REVERT: R 322 MET cc_start: 0.6137 (mmt) cc_final: 0.5896 (mtt) REVERT: R 336 MET cc_start: 0.7217 (ttp) cc_final: 0.6960 (ttt) outliers start: 14 outliers final: 5 residues processed: 254 average time/residue: 0.1383 time to fit residues: 47.7259 Evaluate side-chains 224 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 216 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 339 MET Chi-restraints excluded: chain R residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN C 327 GLN E 343 GLN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 343 GLN ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.137500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.101198 restraints weight = 7414.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.104127 restraints weight = 4764.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.105801 restraints weight = 3635.818| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 5616 Z= 0.371 Angle : 0.835 7.180 7470 Z= 0.440 Chirality : 0.042 0.137 720 Planarity : 0.005 0.032 1026 Dihedral : 6.391 17.628 792 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.79 % Allowed : 36.40 % Favored : 58.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.15), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.11), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP K 334 PHE 0.020 0.003 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.565 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: A 323 MET cc_start: 0.7621 (ttm) cc_final: 0.7063 (ttt) REVERT: B 323 MET cc_start: 0.7106 (ttt) cc_final: 0.6893 (ttt) REVERT: C 311 MET cc_start: 0.8988 (ptp) cc_final: 0.8557 (ptp) REVERT: D 339 MET cc_start: 0.8332 (ptm) cc_final: 0.8076 (ptp) REVERT: E 322 MET cc_start: 0.6933 (mmm) cc_final: 0.4725 (ptp) REVERT: F 307 MET cc_start: 0.9031 (ttt) cc_final: 0.8768 (ttt) REVERT: F 322 MET cc_start: 0.7014 (mmt) cc_final: 0.4324 (ptt) REVERT: G 322 MET cc_start: 0.6837 (mtt) cc_final: 0.5945 (mtt) REVERT: G 323 MET cc_start: 0.7801 (ttm) cc_final: 0.7355 (ttt) REVERT: G 336 MET cc_start: 0.8611 (ttp) cc_final: 0.7922 (ttp) REVERT: H 311 MET cc_start: 0.8929 (ptp) cc_final: 0.8316 (ptp) REVERT: H 327 GLN cc_start: 0.8938 (tp40) cc_final: 0.8288 (tm-30) REVERT: I 327 GLN cc_start: 0.8778 (tp40) cc_final: 0.7997 (tp40) REVERT: J 336 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8188 (ttt) REVERT: K 336 MET cc_start: 0.8469 (ttp) cc_final: 0.8212 (ttt) REVERT: L 327 GLN cc_start: 0.8756 (tp40) cc_final: 0.8344 (tp40) REVERT: M 307 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8119 (ttp) REVERT: M 327 GLN cc_start: 0.8654 (tp40) cc_final: 0.7646 (tp40) REVERT: N 323 MET cc_start: 0.7336 (ttt) cc_final: 0.6862 (ttm) REVERT: N 339 MET cc_start: 0.8561 (ptm) cc_final: 0.8204 (ptp) REVERT: O 327 GLN cc_start: 0.8933 (tp40) cc_final: 0.8662 (tm-30) REVERT: P 322 MET cc_start: 0.5264 (mtt) cc_final: 0.4597 (mtt) REVERT: Q 339 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7754 (mmp) REVERT: R 336 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7961 (ttt) outliers start: 25 outliers final: 15 residues processed: 219 average time/residue: 0.1457 time to fit residues: 43.2772 Evaluate side-chains 218 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain Q residue 339 MET Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 336 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 GLN ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 343 GLN ** N 346 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 = 0.4632 r_free = 0.4632 target = 0.230220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.133725 restraints weight = 7463.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.137974 restraints weight = 4420.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.140467 restraints weight = 3195.511| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5616 Z= 0.115 Angle : 0.631 7.754 7470 Z= 0.304 Chirality : 0.038 0.116 720 Planarity : 0.003 0.025 1026 Dihedral : 5.116 17.417 792 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 4.21 % Allowed : 36.02 % Favored : 59.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 334 PHE 0.013 0.002 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.6150 (mmt) cc_final: 0.4592 (ptp) REVERT: A 323 MET cc_start: 0.7474 (ttm) cc_final: 0.7134 (ttm) REVERT: B 322 MET cc_start: 0.5462 (ptp) cc_final: 0.4699 (pmm) REVERT: B 323 MET cc_start: 0.6992 (ttt) cc_final: 0.6775 (ttt) REVERT: B 327 GLN cc_start: 0.6701 (tm-30) cc_final: 0.6433 (tm-30) REVERT: C 311 MET cc_start: 0.8931 (ptp) cc_final: 0.8498 (ptp) REVERT: C 322 MET cc_start: 0.5943 (ptp) cc_final: 0.5286 (pmm) REVERT: C 323 MET cc_start: 0.6581 (ttt) cc_final: 0.6033 (ttm) REVERT: D 323 MET cc_start: 0.7040 (ttt) cc_final: 0.6567 (ttt) REVERT: D 336 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7916 (ttp) REVERT: D 339 MET cc_start: 0.8497 (ptm) cc_final: 0.8222 (ptp) REVERT: E 307 MET cc_start: 0.8887 (ttm) cc_final: 0.8528 (ttt) REVERT: E 322 MET cc_start: 0.6693 (mmm) cc_final: 0.4851 (ptp) REVERT: E 327 GLN cc_start: 0.8737 (tp40) cc_final: 0.8489 (tp40) REVERT: E 346 GLN cc_start: 0.8696 (mt0) cc_final: 0.7807 (tp40) REVERT: F 307 MET cc_start: 0.9054 (ttt) cc_final: 0.8733 (ttt) REVERT: G 323 MET cc_start: 0.7545 (ttm) cc_final: 0.7037 (ttt) REVERT: G 336 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7396 (ttp) REVERT: G 337 MET cc_start: 0.7670 (mmt) cc_final: 0.7313 (mmt) REVERT: H 327 GLN cc_start: 0.8894 (tp40) cc_final: 0.8076 (tm-30) REVERT: H 336 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7902 (ttt) REVERT: H 346 GLN cc_start: 0.8334 (mt0) cc_final: 0.4673 (mt0) REVERT: I 327 GLN cc_start: 0.8743 (tp40) cc_final: 0.7868 (tp40) REVERT: J 322 MET cc_start: 0.6913 (mmt) cc_final: 0.6367 (mmt) REVERT: J 327 GLN cc_start: 0.8681 (tp40) cc_final: 0.7919 (tp40) REVERT: J 336 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8083 (ttt) REVERT: K 327 GLN cc_start: 0.8993 (tp40) cc_final: 0.7799 (tp40) REVERT: M 323 MET cc_start: 0.7319 (ttt) cc_final: 0.6882 (ttm) REVERT: M 327 GLN cc_start: 0.8611 (tp40) cc_final: 0.7824 (tp-100) REVERT: N 323 MET cc_start: 0.7349 (ttt) cc_final: 0.6876 (ttm) REVERT: N 327 GLN cc_start: 0.8855 (tp40) cc_final: 0.8085 (tp40) REVERT: N 334 TRP cc_start: 0.8306 (p90) cc_final: 0.8062 (p90) REVERT: N 337 MET cc_start: 0.7625 (mmt) cc_final: 0.7374 (mmt) REVERT: N 346 GLN cc_start: 0.8608 (mt0) cc_final: 0.7641 (mt0) REVERT: O 307 MET cc_start: 0.8287 (ttt) cc_final: 0.7951 (ttt) REVERT: O 327 GLN cc_start: 0.8933 (tp40) cc_final: 0.8603 (tm-30) REVERT: P 322 MET cc_start: 0.4780 (mtt) cc_final: 0.4309 (mtt) REVERT: Q 339 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7302 (mmp) outliers start: 22 outliers final: 12 residues processed: 226 average time/residue: 0.1353 time to fit residues: 41.2848 Evaluate side-chains 230 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain Q residue 339 MET Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 chunk 9 optimal weight: 0.0970 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 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 = 0.4650 r_free = 0.4650 target = 0.238852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.132432 restraints weight = 7208.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.136483 restraints weight = 4375.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.139021 restraints weight = 3204.563| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5616 Z= 0.146 Angle : 0.642 7.556 7470 Z= 0.312 Chirality : 0.038 0.119 720 Planarity : 0.003 0.020 1026 Dihedral : 5.080 15.301 792 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.60 % Allowed : 35.82 % Favored : 59.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP E 334 PHE 0.012 0.001 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.6312 (mmt) cc_final: 0.4708 (ptp) REVERT: A 323 MET cc_start: 0.7556 (ttm) cc_final: 0.6994 (ttt) REVERT: B 322 MET cc_start: 0.5833 (ptp) cc_final: 0.5185 (pmm) REVERT: B 327 GLN cc_start: 0.6603 (tm-30) cc_final: 0.6349 (tm-30) REVERT: C 322 MET cc_start: 0.5766 (ptp) cc_final: 0.5043 (pmm) REVERT: C 323 MET cc_start: 0.6562 (ttt) cc_final: 0.5974 (ttm) REVERT: D 323 MET cc_start: 0.7221 (ttt) cc_final: 0.6835 (ttt) REVERT: D 327 GLN cc_start: 0.8682 (tp40) cc_final: 0.8296 (tp40) REVERT: D 336 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8029 (ttp) REVERT: D 339 MET cc_start: 0.8511 (ptm) cc_final: 0.8195 (ptp) REVERT: E 322 MET cc_start: 0.6410 (mmm) cc_final: 0.4699 (ptp) REVERT: E 327 GLN cc_start: 0.8701 (tp40) cc_final: 0.8423 (tp40) REVERT: E 346 GLN cc_start: 0.8703 (mt0) cc_final: 0.8026 (tp40) REVERT: F 307 MET cc_start: 0.9068 (ttt) cc_final: 0.8704 (ttt) REVERT: F 346 GLN cc_start: 0.8443 (mt0) cc_final: 0.7915 (tp40) REVERT: G 336 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7475 (ttp) REVERT: G 337 MET cc_start: 0.7652 (mmt) cc_final: 0.7246 (mmt) REVERT: H 327 GLN cc_start: 0.8881 (tp40) cc_final: 0.8077 (tp40) REVERT: H 336 MET cc_start: 0.8314 (ttp) cc_final: 0.7985 (ttt) REVERT: I 327 GLN cc_start: 0.8749 (tp40) cc_final: 0.8076 (tp40) REVERT: J 327 GLN cc_start: 0.8699 (tp40) cc_final: 0.7994 (tp40) REVERT: J 336 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8042 (ttt) REVERT: K 327 GLN cc_start: 0.8963 (tp40) cc_final: 0.8105 (tp40) REVERT: K 339 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8098 (ptp) REVERT: L 327 GLN cc_start: 0.8723 (tp40) cc_final: 0.8326 (tp40) REVERT: M 323 MET cc_start: 0.7317 (ttt) cc_final: 0.6871 (ttm) REVERT: M 327 GLN cc_start: 0.8665 (tp40) cc_final: 0.7949 (tp-100) REVERT: N 323 MET cc_start: 0.7196 (ttt) cc_final: 0.6760 (ttm) REVERT: N 327 GLN cc_start: 0.8877 (tp40) cc_final: 0.8063 (tp40) REVERT: N 346 GLN cc_start: 0.8482 (mt0) cc_final: 0.7463 (mt0) REVERT: O 327 GLN cc_start: 0.8983 (tp40) cc_final: 0.8602 (tm-30) REVERT: P 322 MET cc_start: 0.4708 (mtt) cc_final: 0.4262 (mtt) REVERT: Q 339 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7353 (mmp) outliers start: 24 outliers final: 17 residues processed: 222 average time/residue: 0.1338 time to fit residues: 40.1149 Evaluate side-chains 232 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 307 MET Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 339 MET Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain Q residue 339 MET Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 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 = 0.4630 r_free = 0.4630 target = 0.226790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.131249 restraints weight = 7383.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.135483 restraints weight = 4420.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.138206 restraints weight = 3221.056| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5616 Z= 0.149 Angle : 0.649 8.214 7470 Z= 0.309 Chirality : 0.038 0.116 720 Planarity : 0.002 0.017 1026 Dihedral : 5.007 16.192 792 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.98 % Allowed : 33.91 % Favored : 61.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 334 PHE 0.011 0.002 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.6034 (mmt) cc_final: 0.4741 (ptp) REVERT: A 323 MET cc_start: 0.7570 (ttm) cc_final: 0.7008 (ttt) REVERT: B 322 MET cc_start: 0.5411 (ptp) cc_final: 0.5186 (pmm) REVERT: B 327 GLN cc_start: 0.6521 (tm-30) cc_final: 0.6242 (tm-30) REVERT: C 323 MET cc_start: 0.6575 (ttt) cc_final: 0.6100 (ttm) REVERT: D 323 MET cc_start: 0.7259 (ttt) cc_final: 0.6660 (ttt) REVERT: D 327 GLN cc_start: 0.8674 (tp40) cc_final: 0.8322 (tp40) REVERT: D 336 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8031 (ttp) REVERT: D 339 MET cc_start: 0.8475 (ptm) cc_final: 0.8141 (ptp) REVERT: E 322 MET cc_start: 0.6388 (mmm) cc_final: 0.4559 (ptp) REVERT: E 323 MET cc_start: 0.7455 (ttt) cc_final: 0.6839 (ttt) REVERT: E 327 GLN cc_start: 0.8694 (tp40) cc_final: 0.8367 (tp40) REVERT: E 346 GLN cc_start: 0.8667 (mt0) cc_final: 0.7955 (tp40) REVERT: F 346 GLN cc_start: 0.8527 (mt0) cc_final: 0.7884 (tp40) REVERT: G 323 MET cc_start: 0.7635 (ttm) cc_final: 0.7261 (ttt) REVERT: G 336 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7527 (ttp) REVERT: G 337 MET cc_start: 0.7744 (mmt) cc_final: 0.7290 (mmt) REVERT: H 327 GLN cc_start: 0.8865 (tp40) cc_final: 0.8087 (tp40) REVERT: H 336 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7828 (ttt) REVERT: I 327 GLN cc_start: 0.8761 (tp40) cc_final: 0.8041 (tp40) REVERT: I 337 MET cc_start: 0.8068 (mmt) cc_final: 0.7697 (mmt) REVERT: J 322 MET cc_start: 0.7023 (mmt) cc_final: 0.6632 (mmt) REVERT: J 327 GLN cc_start: 0.8745 (tp40) cc_final: 0.8079 (tp40) REVERT: J 336 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7936 (ttt) REVERT: K 327 GLN cc_start: 0.8870 (tp40) cc_final: 0.8155 (tp40) REVERT: L 327 GLN cc_start: 0.8737 (tp40) cc_final: 0.8373 (tp40) REVERT: L 337 MET cc_start: 0.7915 (mmt) cc_final: 0.7652 (mmt) REVERT: M 323 MET cc_start: 0.7349 (ttt) cc_final: 0.6921 (ttm) REVERT: M 327 GLN cc_start: 0.8665 (tp40) cc_final: 0.7972 (tp-100) REVERT: N 323 MET cc_start: 0.7303 (ttt) cc_final: 0.6869 (ttm) REVERT: N 327 GLN cc_start: 0.8864 (tp40) cc_final: 0.8074 (tp40) REVERT: N 337 MET cc_start: 0.7930 (mtt) cc_final: 0.7709 (mtt) REVERT: N 346 GLN cc_start: 0.8527 (mt0) cc_final: 0.7481 (mt0) REVERT: O 327 GLN cc_start: 0.8963 (tp40) cc_final: 0.8547 (tm-30) REVERT: P 322 MET cc_start: 0.4451 (mtt) cc_final: 0.4110 (mtt) REVERT: Q 339 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7344 (mmp) REVERT: R 322 MET cc_start: 0.5551 (mtt) cc_final: 0.4914 (mtt) outliers start: 26 outliers final: 19 residues processed: 223 average time/residue: 0.1360 time to fit residues: 40.9384 Evaluate side-chains 235 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain Q residue 339 MET Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 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 = 0.4624 r_free = 0.4624 target = 0.233110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.125350 restraints weight = 7329.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.129366 restraints weight = 4533.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.131746 restraints weight = 3358.546| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 5616 Z= 0.228 Angle : 0.701 8.161 7470 Z= 0.344 Chirality : 0.039 0.121 720 Planarity : 0.003 0.018 1026 Dihedral : 5.466 16.339 792 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.75 % Allowed : 33.91 % Favored : 60.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.15), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.11), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 334 PHE 0.011 0.002 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.5507 (mmt) cc_final: 0.4134 (ptp) REVERT: A 323 MET cc_start: 0.7613 (ttm) cc_final: 0.7009 (ttt) REVERT: B 322 MET cc_start: 0.5661 (ptp) cc_final: 0.5158 (pmm) REVERT: B 327 GLN cc_start: 0.7007 (tm-30) cc_final: 0.6647 (tm-30) REVERT: D 323 MET cc_start: 0.7419 (ttt) cc_final: 0.6861 (ttt) REVERT: D 327 GLN cc_start: 0.8682 (tp40) cc_final: 0.8202 (tp40) REVERT: D 339 MET cc_start: 0.8433 (ptm) cc_final: 0.8082 (ptp) REVERT: E 322 MET cc_start: 0.6627 (mmm) cc_final: 0.4463 (ptp) REVERT: E 327 GLN cc_start: 0.8815 (tp40) cc_final: 0.8442 (tp40) REVERT: E 346 GLN cc_start: 0.8698 (mt0) cc_final: 0.7961 (tp40) REVERT: F 307 MET cc_start: 0.8829 (ttt) cc_final: 0.8437 (ttt) REVERT: F 337 MET cc_start: 0.7994 (mmt) cc_final: 0.7760 (mmt) REVERT: G 323 MET cc_start: 0.7593 (ttm) cc_final: 0.7225 (ttt) REVERT: G 327 GLN cc_start: 0.8911 (tp40) cc_final: 0.8059 (tp40) REVERT: G 336 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8001 (ttp) REVERT: H 311 MET cc_start: 0.9021 (ptp) cc_final: 0.8241 (ptp) REVERT: H 327 GLN cc_start: 0.8833 (tp40) cc_final: 0.8045 (tp40) REVERT: H 336 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7977 (ttt) REVERT: I 327 GLN cc_start: 0.8734 (tp40) cc_final: 0.7834 (tp40) REVERT: J 327 GLN cc_start: 0.8723 (tp40) cc_final: 0.7933 (tp40) REVERT: J 336 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7953 (ttt) REVERT: K 327 GLN cc_start: 0.8878 (tp40) cc_final: 0.8150 (tp40) REVERT: L 327 GLN cc_start: 0.8763 (tp40) cc_final: 0.8355 (tp40) REVERT: M 307 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7955 (ttp) REVERT: M 323 MET cc_start: 0.7347 (ttt) cc_final: 0.6910 (ttm) REVERT: M 327 GLN cc_start: 0.8741 (tp40) cc_final: 0.8060 (tp-100) REVERT: N 323 MET cc_start: 0.7137 (ttt) cc_final: 0.6689 (ttm) REVERT: N 327 GLN cc_start: 0.8882 (tp40) cc_final: 0.7978 (tp40) REVERT: N 346 GLN cc_start: 0.8525 (mt0) cc_final: 0.7746 (mt0) REVERT: O 327 GLN cc_start: 0.8970 (tp40) cc_final: 0.8602 (tm-30) REVERT: P 322 MET cc_start: 0.4562 (mtt) cc_final: 0.4239 (mtt) REVERT: P 336 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7507 (ttt) REVERT: P 337 MET cc_start: 0.7881 (mtt) cc_final: 0.6993 (mtt) REVERT: Q 337 MET cc_start: 0.7686 (mtt) cc_final: 0.7438 (mtt) REVERT: Q 339 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7660 (mmp) REVERT: R 322 MET cc_start: 0.5280 (mtt) cc_final: 0.4686 (mtt) outliers start: 30 outliers final: 20 residues processed: 218 average time/residue: 0.1365 time to fit residues: 40.2243 Evaluate side-chains 233 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain Q residue 336 MET Chi-restraints excluded: chain Q residue 339 MET Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 331 GLN ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 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 = 0.4846 r_free = 0.4846 target = 0.307011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.232918 restraints weight = 8401.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.231784 restraints weight = 13330.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.232322 restraints weight = 13670.789| |-----------------------------------------------------------------------------| r_work (final): 0.4696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5616 Z= 0.125 Angle : 0.638 8.165 7470 Z= 0.299 Chirality : 0.038 0.113 720 Planarity : 0.002 0.017 1026 Dihedral : 4.913 18.377 792 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.79 % Allowed : 35.06 % Favored : 60.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 334 PHE 0.010 0.002 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.7110 (ttm) cc_final: 0.6859 (ttt) REVERT: D 322 MET cc_start: 0.6566 (mmt) cc_final: 0.3950 (ptp) REVERT: D 323 MET cc_start: 0.7119 (ttt) cc_final: 0.6769 (ttt) REVERT: E 322 MET cc_start: 0.5930 (mmm) cc_final: 0.4799 (ptp) REVERT: E 323 MET cc_start: 0.7098 (ttt) cc_final: 0.6763 (ttt) REVERT: G 327 GLN cc_start: 0.8272 (tp40) cc_final: 0.7948 (tp40) REVERT: G 336 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8027 (ttp) REVERT: H 311 MET cc_start: 0.8746 (ptp) cc_final: 0.8480 (ptp) REVERT: H 327 GLN cc_start: 0.8266 (tp40) cc_final: 0.7909 (tp40) REVERT: H 336 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7825 (ttt) REVERT: I 327 GLN cc_start: 0.8266 (tp40) cc_final: 0.7939 (tp40) REVERT: J 336 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7533 (ttt) REVERT: M 323 MET cc_start: 0.7173 (ttt) cc_final: 0.6888 (ttm) REVERT: N 323 MET cc_start: 0.7100 (ttt) cc_final: 0.6819 (ttm) REVERT: N 327 GLN cc_start: 0.8154 (tp40) cc_final: 0.7941 (tp40) REVERT: N 346 GLN cc_start: 0.8213 (mt0) cc_final: 0.7464 (mt0) REVERT: P 322 MET cc_start: 0.5165 (mtt) cc_final: 0.4872 (mtt) REVERT: P 337 MET cc_start: 0.7089 (mtt) cc_final: 0.6851 (mtt) REVERT: Q 339 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7558 (mmp) REVERT: R 322 MET cc_start: 0.6054 (mtt) cc_final: 0.5614 (mtt) outliers start: 25 outliers final: 20 residues processed: 220 average time/residue: 0.1374 time to fit residues: 40.9339 Evaluate side-chains 228 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 339 MET Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain Q residue 336 MET Chi-restraints excluded: chain Q residue 339 MET Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 339 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 GLN ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 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 = 0.4796 r_free = 0.4796 target = 0.296911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.220003 restraints weight = 8485.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.218595 restraints weight = 14452.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.219278 restraints weight = 14643.371| |-----------------------------------------------------------------------------| r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 5616 Z= 0.290 Angle : 0.776 8.353 7470 Z= 0.392 Chirality : 0.041 0.116 720 Planarity : 0.003 0.021 1026 Dihedral : 5.754 18.520 792 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.56 % Allowed : 36.02 % Favored : 58.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.15), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP K 334 PHE 0.013 0.002 PHE P 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.5660 (ptp) cc_final: 0.5386 (pmm) REVERT: A 323 MET cc_start: 0.7017 (ttm) cc_final: 0.6747 (ttt) REVERT: C 311 MET cc_start: 0.8979 (ptp) cc_final: 0.8494 (ptp) REVERT: D 323 MET cc_start: 0.7264 (ttt) cc_final: 0.6907 (ttt) REVERT: E 322 MET cc_start: 0.5774 (mmm) cc_final: 0.4588 (ptp) REVERT: G 327 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8117 (tp40) REVERT: G 336 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8071 (ttp) REVERT: H 311 MET cc_start: 0.8864 (ptp) cc_final: 0.8187 (ptp) REVERT: H 336 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7946 (ttt) REVERT: I 327 GLN cc_start: 0.8337 (tp40) cc_final: 0.7835 (tp40) REVERT: J 336 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7527 (ttt) REVERT: K 346 GLN cc_start: 0.7933 (mt0) cc_final: 0.7364 (tt0) REVERT: M 307 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8481 (ttp) REVERT: M 323 MET cc_start: 0.7066 (ttt) cc_final: 0.6765 (ttm) REVERT: N 323 MET cc_start: 0.7097 (ttt) cc_final: 0.6778 (ttm) REVERT: N 327 GLN cc_start: 0.8291 (tp40) cc_final: 0.7940 (tp40) REVERT: N 346 GLN cc_start: 0.8238 (mt0) cc_final: 0.7179 (mt0) REVERT: P 322 MET cc_start: 0.5424 (mtt) cc_final: 0.5061 (mtt) REVERT: Q 337 MET cc_start: 0.7183 (mtt) cc_final: 0.6971 (mmp) REVERT: R 322 MET cc_start: 0.5748 (mtt) cc_final: 0.5179 (mtt) outliers start: 29 outliers final: 21 residues processed: 205 average time/residue: 0.1331 time to fit residues: 37.0767 Evaluate side-chains 222 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 327 GLN Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 339 MET Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain Q residue 336 MET Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 339 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 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 = 0.4841 r_free = 0.4841 target = 0.303618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 154)---------------| | r_work = 0.4987 r_free = 0.4987 target = 0.217365 restraints weight = 8512.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.217271 restraints weight = 9701.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.217271 restraints weight = 9619.312| |-----------------------------------------------------------------------------| r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5616 Z= 0.186 Angle : 0.745 8.761 7470 Z= 0.363 Chirality : 0.039 0.114 720 Planarity : 0.003 0.021 1026 Dihedral : 5.431 20.598 792 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.36 % Allowed : 34.87 % Favored : 59.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 334 PHE 0.011 0.002 PHE C 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 322 MET cc_start: 0.5416 (ptp) cc_final: 0.5095 (pmm) REVERT: C 307 MET cc_start: 0.8677 (tpp) cc_final: 0.8386 (tpt) REVERT: C 311 MET cc_start: 0.8873 (ptp) cc_final: 0.8405 (ptp) REVERT: D 322 MET cc_start: 0.6529 (mmt) cc_final: 0.4231 (ptp) REVERT: D 323 MET cc_start: 0.7380 (ttt) cc_final: 0.6999 (ttt) REVERT: E 322 MET cc_start: 0.5930 (mmm) cc_final: 0.4840 (ptp) REVERT: E 323 MET cc_start: 0.7164 (ttt) cc_final: 0.6777 (ttt) REVERT: G 327 GLN cc_start: 0.8336 (tp40) cc_final: 0.8003 (tp40) REVERT: G 336 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8124 (ttp) REVERT: H 311 MET cc_start: 0.8963 (ptp) cc_final: 0.8648 (ptp) REVERT: H 336 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7977 (ttt) REVERT: I 327 GLN cc_start: 0.8342 (tp40) cc_final: 0.7751 (tp40) REVERT: J 336 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7765 (ttt) REVERT: M 307 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8413 (ttp) REVERT: M 323 MET cc_start: 0.7175 (ttt) cc_final: 0.6888 (ttm) REVERT: N 323 MET cc_start: 0.7134 (ttt) cc_final: 0.6823 (ttm) REVERT: N 345 ASN cc_start: 0.8816 (m110) cc_final: 0.8600 (m-40) REVERT: P 322 MET cc_start: 0.5380 (mtt) cc_final: 0.5078 (mtt) REVERT: R 322 MET cc_start: 0.5723 (mtt) cc_final: 0.5351 (mtt) outliers start: 28 outliers final: 20 residues processed: 206 average time/residue: 0.1354 time to fit residues: 37.9668 Evaluate side-chains 217 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain Q residue 336 MET Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 339 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 56 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 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 = 0.4884 r_free = 0.4884 target = 0.308982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 157)---------------| | r_work = 0.5018 r_free = 0.5018 target = 0.223501 restraints weight = 8509.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.223673 restraints weight = 9070.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.223673 restraints weight = 9091.507| |-----------------------------------------------------------------------------| r_work (final): 0.4723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.7446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5616 Z= 0.143 Angle : 0.739 9.072 7470 Z= 0.353 Chirality : 0.039 0.118 720 Planarity : 0.002 0.018 1026 Dihedral : 5.021 20.858 792 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.41 % Allowed : 36.59 % Favored : 59.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 334 PHE 0.011 0.001 PHE C 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.43 seconds wall clock time: 37 minutes 6.15 seconds (2226.15 seconds total)