Starting phenix.real_space_refine on Fri Dec 27 14:51:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxb_18717/12_2024/8qxb_18717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxb_18717/12_2024/8qxb_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_18717/12_2024/8qxb_18717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxb_18717/12_2024/8qxb_18717.map" model { file = "/net/cci-nas-00/data/ceres_data/8qxb_18717/12_2024/8qxb_18717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxb_18717/12_2024/8qxb_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-5532/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: 1.76, per 1000 atoms: 0.32 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: 1.25 Conformation dependent library (CDL) restraints added in 719.3 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: 0.54 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: 0.14 Time building geometry restraints manager: 1.46 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' 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: 1.070 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.440 Find NCS groups from input model: 0.180 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- 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 : 0.604 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: 0.1357 time to fit residues: 58.7483 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 : 0.604 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 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 : 0.644 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: C 336 MET cc_start: 0.5705 (ttm) cc_final: 0.5490 (ttt) REVERT: C 337 MET cc_start: 0.5876 (ppp) cc_final: 0.5507 (ppp) REVERT: D 336 MET cc_start: 0.8078 (ttp) cc_final: 0.7731 (ttt) REVERT: E 322 MET cc_start: 0.5886 (mmm) cc_final: 0.4856 (ptp) REVERT: P 336 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6601 (ttt) REVERT: R 336 MET cc_start: 0.6646 (ttp) cc_final: 0.6396 (ttt) outliers start: 14 outliers final: 5 residues processed: 254 average time/residue: 0.1400 time to fit residues: 47.9315 Evaluate side-chains 218 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 212 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 R residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 343 GLN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 327 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 5616 Z= 0.382 Angle : 0.864 6.819 7470 Z= 0.455 Chirality : 0.043 0.148 720 Planarity : 0.005 0.034 1026 Dihedral : 6.260 16.858 792 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.36 % Allowed : 35.06 % 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: -4.50 (0.15), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.11), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP G 334 PHE 0.021 0.003 PHE R 316 *********************** 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 235 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 MET cc_start: 0.6714 (ttt) cc_final: 0.6462 (ttt) REVERT: C 311 MET cc_start: 0.8695 (ptp) cc_final: 0.8408 (ptp) REVERT: C 336 MET cc_start: 0.5566 (ttm) cc_final: 0.5359 (ttm) REVERT: E 322 MET cc_start: 0.6011 (mmm) cc_final: 0.5234 (ptt) REVERT: F 322 MET cc_start: 0.6207 (mmt) cc_final: 0.4325 (ptp) REVERT: G 322 MET cc_start: 0.6073 (mtt) cc_final: 0.5870 (mtt) REVERT: G 336 MET cc_start: 0.8424 (ttp) cc_final: 0.7841 (ttp) REVERT: H 311 MET cc_start: 0.8773 (ptp) cc_final: 0.8476 (ptp) REVERT: J 336 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8044 (ttt) REVERT: M 336 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8268 (ttp) REVERT: P 322 MET cc_start: 0.5730 (mtt) cc_final: 0.5290 (mtt) REVERT: Q 307 MET cc_start: 0.8435 (ttm) cc_final: 0.8168 (ttt) REVERT: R 313 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8626 (m-80) REVERT: R 336 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7588 (ttt) outliers start: 28 outliers final: 20 residues processed: 218 average time/residue: 0.1348 time to fit residues: 39.9748 Evaluate side-chains 213 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain I residue 305 SER 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 336 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 R residue 305 SER Chi-restraints excluded: chain R residue 313 PHE 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 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.0070 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN F 327 GLN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 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** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5616 Z= 0.126 Angle : 0.663 7.765 7470 Z= 0.323 Chirality : 0.038 0.116 720 Planarity : 0.003 0.025 1026 Dihedral : 5.050 15.126 792 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.41 % Allowed : 34.10 % Favored : 61.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 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 244 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: B 322 MET cc_start: 0.4294 (ptp) cc_final: 0.4049 (pmm) REVERT: B 323 MET cc_start: 0.6301 (ttt) cc_final: 0.6065 (ttt) REVERT: D 307 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8185 (ttm) REVERT: D 322 MET cc_start: 0.5534 (mmt) cc_final: 0.4565 (ptp) REVERT: E 307 MET cc_start: 0.8586 (ttm) cc_final: 0.8159 (ttt) REVERT: E 322 MET cc_start: 0.5551 (mmm) cc_final: 0.5323 (ptp) REVERT: G 336 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7842 (ttp) REVERT: I 346 GLN cc_start: 0.6362 (mt0) cc_final: 0.5721 (mt0) REVERT: J 336 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8176 (ttt) REVERT: L 336 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7968 (ttp) REVERT: M 336 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7891 (ttp) REVERT: P 322 MET cc_start: 0.5596 (mtt) cc_final: 0.5271 (mtt) REVERT: Q 307 MET cc_start: 0.8456 (ttm) cc_final: 0.8129 (ttt) outliers start: 23 outliers final: 14 residues processed: 227 average time/residue: 0.1338 time to fit residues: 41.1621 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 : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G 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 L residue 336 MET Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 336 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 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP 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 57 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 0.0010 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN G 327 GLN G 343 GLN ** I 343 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** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 346 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5616 Z= 0.182 Angle : 0.698 7.375 7470 Z= 0.350 Chirality : 0.039 0.124 720 Planarity : 0.003 0.022 1026 Dihedral : 5.236 17.810 792 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.75 % Allowed : 34.10 % 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: -4.32 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 334 PHE 0.013 0.002 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 241 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.625 Fit side-chains REVERT: B 322 MET cc_start: 0.4556 (ptp) cc_final: 0.4318 (pmm) REVERT: D 322 MET cc_start: 0.5245 (mmt) cc_final: 0.4438 (ptp) REVERT: D 336 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8011 (ttt) REVERT: E 322 MET cc_start: 0.5628 (mmm) cc_final: 0.5187 (ptp) REVERT: F 307 MET cc_start: 0.8089 (ttt) cc_final: 0.7728 (ttt) REVERT: G 336 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7928 (ttp) REVERT: H 311 MET cc_start: 0.8797 (ptp) cc_final: 0.8569 (ptp) REVERT: H 322 MET cc_start: 0.6582 (mmt) cc_final: 0.6295 (mmt) REVERT: J 336 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8163 (ttt) REVERT: M 336 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: N 337 MET cc_start: 0.6957 (mtt) cc_final: 0.6519 (mtt) REVERT: P 322 MET cc_start: 0.5394 (mtt) cc_final: 0.5112 (mtt) REVERT: Q 307 MET cc_start: 0.8474 (ttm) cc_final: 0.8169 (ttt) REVERT: R 322 MET cc_start: 0.5844 (mtt) cc_final: 0.5366 (mtt) outliers start: 30 outliers final: 21 residues processed: 219 average time/residue: 0.1351 time to fit residues: 40.1200 Evaluate side-chains 222 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain C residue 327 GLN 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 I residue 305 SER 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 336 MET Chi-restraints excluded: chain M residue 346 GLN 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 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 23 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 0.0070 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 GLN ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5616 Z= 0.129 Angle : 0.665 7.815 7470 Z= 0.325 Chirality : 0.038 0.116 720 Planarity : 0.002 0.017 1026 Dihedral : 4.859 16.951 792 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.41 % Allowed : 35.06 % Favored : 60.54 % 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: -4.25 (0.17), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.13), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 334 PHE 0.012 0.001 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 237 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.638 Fit side-chains REVERT: C 336 MET cc_start: 0.5286 (ttm) cc_final: 0.4792 (ttt) REVERT: D 322 MET cc_start: 0.5047 (mmt) cc_final: 0.4615 (ptp) REVERT: D 336 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7925 (ttt) REVERT: F 307 MET cc_start: 0.7996 (ttt) cc_final: 0.7678 (ttt) REVERT: G 336 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7900 (ttp) REVERT: J 336 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8091 (ttp) REVERT: J 345 ASN cc_start: 0.7847 (m-40) cc_final: 0.7606 (m110) REVERT: L 336 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7809 (ttp) REVERT: M 336 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7878 (ttp) REVERT: Q 307 MET cc_start: 0.8547 (ttm) cc_final: 0.8212 (ttp) REVERT: R 322 MET cc_start: 0.5547 (mtt) cc_final: 0.5149 (mtt) outliers start: 23 outliers final: 15 residues processed: 219 average time/residue: 0.1340 time to fit residues: 39.7354 Evaluate side-chains 220 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 L residue 305 SER Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 336 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 R residue 305 SER 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 7 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN ** D 327 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** ** G 327 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** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.7238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5616 Z= 0.124 Angle : 0.665 8.106 7470 Z= 0.319 Chirality : 0.038 0.117 720 Planarity : 0.002 0.016 1026 Dihedral : 4.823 18.366 792 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.02 % Allowed : 35.44 % Favored : 60.54 % 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: -4.29 (0.17), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.13), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 334 PHE 0.011 0.001 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 230 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.491 Fit side-chains REVERT: C 336 MET cc_start: 0.5420 (ttm) cc_final: 0.5011 (ttt) REVERT: C 337 MET cc_start: 0.5146 (ppp) cc_final: 0.4805 (ppp) REVERT: D 336 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7869 (ttt) REVERT: F 307 MET cc_start: 0.7996 (ttt) cc_final: 0.7610 (ttt) REVERT: G 336 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7948 (ttp) REVERT: H 311 MET cc_start: 0.8771 (ptp) cc_final: 0.8533 (ptp) REVERT: L 336 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7416 (ttp) REVERT: M 336 MET cc_start: 0.7948 (ttp) cc_final: 0.7710 (ttp) REVERT: N 337 MET cc_start: 0.6873 (mtt) cc_final: 0.6467 (mtt) REVERT: Q 307 MET cc_start: 0.8552 (ttm) cc_final: 0.8195 (ttp) outliers start: 21 outliers final: 16 residues processed: 213 average time/residue: 0.1373 time to fit residues: 39.5770 Evaluate side-chains 216 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 GLN 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 H residue 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 336 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 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** ** 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** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.7386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 5616 Z= 0.292 Angle : 0.786 7.615 7470 Z= 0.403 Chirality : 0.041 0.118 720 Planarity : 0.003 0.020 1026 Dihedral : 5.843 17.563 792 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.36 % Allowed : 33.91 % Favored : 60.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.15), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.11), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP D 334 PHE 0.017 0.002 PHE R 316 *********************** 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 226 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.530 Fit side-chains REVERT: A 307 MET cc_start: 0.8442 (ttm) cc_final: 0.8189 (ttp) REVERT: D 336 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8070 (ttt) REVERT: G 336 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7923 (ttp) REVERT: H 311 MET cc_start: 0.9081 (ptp) cc_final: 0.8710 (ptp) REVERT: J 336 MET cc_start: 0.7952 (ttp) cc_final: 0.7705 (ttt) REVERT: M 336 MET cc_start: 0.8464 (ttp) cc_final: 0.8202 (ttp) REVERT: P 337 MET cc_start: 0.7132 (mtt) cc_final: 0.6915 (mtt) REVERT: Q 307 MET cc_start: 0.8499 (ttm) cc_final: 0.8192 (ttp) outliers start: 28 outliers final: 22 residues processed: 206 average time/residue: 0.1391 time to fit residues: 38.9807 Evaluate side-chains 212 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 GLN 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 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 332 SER Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 346 GLN 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 N residue 336 MET 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 311 MET Chi-restraints excluded: chain Q residue 334 TRP 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 66 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.7560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5616 Z= 0.153 Angle : 0.709 7.856 7470 Z= 0.344 Chirality : 0.039 0.113 720 Planarity : 0.003 0.019 1026 Dihedral : 5.200 20.419 792 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.98 % Allowed : 33.33 % Favored : 61.69 % 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: -4.68 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 334 PHE 0.011 0.002 PHE C 313 *********************** 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 229 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.577 Fit side-chains REVERT: C 307 MET cc_start: 0.8527 (tpp) cc_final: 0.8319 (tpt) REVERT: C 336 MET cc_start: 0.5524 (ttm) cc_final: 0.5015 (ttt) REVERT: D 336 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8048 (ttt) REVERT: G 336 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7829 (ttt) REVERT: H 311 MET cc_start: 0.9033 (ptp) cc_final: 0.8769 (ptp) REVERT: K 346 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.6764 (mm-40) REVERT: M 336 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7953 (ttp) REVERT: P 336 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6819 (ttt) REVERT: Q 307 MET cc_start: 0.8515 (ttm) cc_final: 0.8214 (ttp) outliers start: 26 outliers final: 20 residues processed: 210 average time/residue: 0.1347 time to fit residues: 38.4342 Evaluate side-chains 221 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 332 SER Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 346 GLN Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 336 MET Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 336 MET 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 R residue 305 SER Chi-restraints excluded: chain R residue 316 PHE 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 32 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 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** ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.7730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5616 Z= 0.146 Angle : 0.716 9.300 7470 Z= 0.344 Chirality : 0.039 0.118 720 Planarity : 0.002 0.018 1026 Dihedral : 5.063 21.500 792 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.79 % Allowed : 34.87 % 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: -4.72 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (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 233 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.574 Fit side-chains REVERT: C 307 MET cc_start: 0.8418 (tpp) cc_final: 0.8186 (tpt) REVERT: C 336 MET cc_start: 0.5492 (ttm) cc_final: 0.5025 (ttt) REVERT: H 311 MET cc_start: 0.8701 (ptp) cc_final: 0.8310 (ptp) REVERT: I 322 MET cc_start: 0.5679 (mmt) cc_final: 0.5398 (mmt) REVERT: K 346 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6944 (mm-40) REVERT: M 336 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7607 (ttp) REVERT: P 336 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6691 (ttt) REVERT: Q 307 MET cc_start: 0.8456 (ttm) cc_final: 0.8191 (ttp) outliers start: 25 outliers final: 18 residues processed: 213 average time/residue: 0.1355 time to fit residues: 39.0975 Evaluate side-chains 221 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 346 GLN Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 336 MET Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 336 MET 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 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 52 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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** ** L 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 346 GLN ** O 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.301670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.5002 r_free = 0.5002 target = 0.214763 restraints weight = 8457.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.214825 restraints weight = 9170.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.214824 restraints weight = 9319.934| |-----------------------------------------------------------------------------| r_work (final): 0.4676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.7796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5616 Z= 0.240 Angle : 0.782 8.601 7470 Z= 0.389 Chirality : 0.040 0.115 720 Planarity : 0.003 0.018 1026 Dihedral : 5.612 20.016 792 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.41 % Allowed : 35.63 % Favored : 59.96 % 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: -4.89 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 334 PHE 0.013 0.002 PHE Q 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1605.56 seconds wall clock time: 29 minutes 50.64 seconds (1790.64 seconds total)