Starting phenix.real_space_refine on Sun Mar 17 18:19:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/03_2024/6qoz_4610.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/03_2024/6qoz_4610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/03_2024/6qoz_4610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/03_2024/6qoz_4610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/03_2024/6qoz_4610.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qoz_4610/03_2024/6qoz_4610.pdb" } resolution = 3.4 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= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 655 atoms to isotropic. 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 125 5.16 5 C 11466 2.51 5 N 3011 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17987 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "B" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "D" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "E" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "G" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "H" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1476 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 168} Chain: "I" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2857 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain: "C" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 655 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Time building chain proxies: 9.56, per 1000 atoms: 0.53 Number of scatterers: 17987 At special positions: 0 Unit cell: (141.4, 152.6, 175, 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 125 16.00 O 3385 8.00 N 3011 7.00 C 11466 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 - 3.50 Amino acid : False - 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: 6.24 Conformation dependent library (CDL) restraints added in 3.2 seconds 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4288 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 13.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.512A pdb=" N ASN B 52 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 103 through 109 removed outlier: 4.584A pdb=" N SER B 109 " --> pdb=" O TYR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 230 through 237 removed outlier: 3.500A pdb=" N SER B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'E' and resid 4 through 8 Processing helix chain 'E' and resid 48 through 52 removed outlier: 3.512A pdb=" N ASN E 52 " --> pdb=" O ASP E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 103 through 109 removed outlier: 4.586A pdb=" N SER E 109 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'G' and resid 4 through 8 Processing helix chain 'G' and resid 48 through 52 removed outlier: 3.512A pdb=" N ASN G 52 " --> pdb=" O ASP G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 65 Processing helix chain 'G' and resid 103 through 109 removed outlier: 4.586A pdb=" N SER G 109 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 144 Processing helix chain 'G' and resid 230 through 237 removed outlier: 3.500A pdb=" N SER G 237 " --> pdb=" O ASN G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 300 through 304 Processing helix chain 'H' and resid 54 through 62 Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 137 through 141 Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 48 through 52 removed outlier: 3.513A pdb=" N ASN I 52 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 65 Processing helix chain 'I' and resid 103 through 109 removed outlier: 4.585A pdb=" N SER I 109 " --> pdb=" O TYR I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 144 Processing helix chain 'I' and resid 230 through 237 Processing helix chain 'I' and resid 277 through 281 Processing helix chain 'I' and resid 300 through 304 Processing helix chain 'C' and resid 33 through 53 135 hydrogen bonds defined for protein. 273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4973 1.33 - 1.46: 4187 1.46 - 1.58: 9102 1.58 - 1.70: 0 1.70 - 1.83: 194 Bond restraints: 18456 Sorted by residual: bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.531 -0.080 1.60e-02 3.91e+03 2.53e+01 bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.530 -0.079 1.60e-02 3.91e+03 2.46e+01 bond pdb=" N GLY D 1 " pdb=" CA GLY D 1 " ideal model delta sigma weight residual 1.451 1.530 -0.079 1.60e-02 3.91e+03 2.46e+01 bond pdb=" N GLY F 1 " pdb=" CA GLY F 1 " ideal model delta sigma weight residual 1.451 1.530 -0.079 1.60e-02 3.91e+03 2.46e+01 bond pdb=" CA PRO D 187 " pdb=" C PRO D 187 " ideal model delta sigma weight residual 1.517 1.545 -0.028 6.70e-03 2.23e+04 1.81e+01 ... (remaining 18451 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.13: 432 104.13 - 111.60: 7425 111.60 - 119.07: 7259 119.07 - 126.55: 9676 126.55 - 134.02: 349 Bond angle restraints: 25141 Sorted by residual: angle pdb=" N ARG I 367 " pdb=" CA ARG I 367 " pdb=" C ARG I 367 " ideal model delta sigma weight residual 110.55 118.98 -8.43 1.35e+00 5.49e-01 3.90e+01 angle pdb=" N ARG E 367 " pdb=" CA ARG E 367 " pdb=" C ARG E 367 " ideal model delta sigma weight residual 110.55 118.98 -8.43 1.35e+00 5.49e-01 3.90e+01 angle pdb=" N ARG G 367 " pdb=" CA ARG G 367 " pdb=" C ARG G 367 " ideal model delta sigma weight residual 110.55 118.94 -8.39 1.35e+00 5.49e-01 3.87e+01 angle pdb=" N ARG B 367 " pdb=" CA ARG B 367 " pdb=" C ARG B 367 " ideal model delta sigma weight residual 110.55 118.93 -8.38 1.35e+00 5.49e-01 3.85e+01 angle pdb=" N GLY C 71 " pdb=" CA GLY C 71 " pdb=" C GLY C 71 " ideal model delta sigma weight residual 112.52 104.58 7.94 1.37e+00 5.33e-01 3.36e+01 ... (remaining 25136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 9750 17.68 - 35.36: 846 35.36 - 53.04: 186 53.04 - 70.72: 69 70.72 - 88.40: 20 Dihedral angle restraints: 10871 sinusoidal: 4222 harmonic: 6649 Sorted by residual: dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N ASP D 9 " pdb=" CA ASP D 9 " ideal model delta harmonic sigma weight residual 180.00 -153.20 -26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA SER A 8 " pdb=" C SER A 8 " pdb=" N ASP A 9 " pdb=" CA ASP A 9 " ideal model delta harmonic sigma weight residual 180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA SER H 8 " pdb=" C SER H 8 " pdb=" N ASP H 9 " pdb=" CA ASP H 9 " ideal model delta harmonic sigma weight residual -180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 10868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2338 0.121 - 0.242: 424 0.242 - 0.362: 22 0.362 - 0.483: 4 0.483 - 0.604: 4 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CA ASN B 174 " pdb=" N ASN B 174 " pdb=" C ASN B 174 " pdb=" CB ASN B 174 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" CA ASN I 174 " pdb=" N ASN I 174 " pdb=" C ASN I 174 " pdb=" CB ASN I 174 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.11e+00 chirality pdb=" CA ASN G 174 " pdb=" N ASN G 174 " pdb=" C ASN G 174 " pdb=" CB ASN G 174 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.06e+00 ... (remaining 2789 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 255 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO G 256 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 256 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 256 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 255 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO I 256 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO I 256 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 256 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 255 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO E 256 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 256 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 256 " 0.029 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 23 1.97 - 2.71: 591 2.71 - 3.44: 24257 3.44 - 4.17: 46687 4.17 - 4.90: 80930 Nonbonded interactions: 152488 Sorted by model distance: nonbonded pdb=" CA GLY B 53 " pdb=" CD2 LEU C 35 " model vdw 1.243 3.860 nonbonded pdb=" O GLY B 53 " pdb=" CD1 LEU C 35 " model vdw 1.334 3.460 nonbonded pdb=" O GLY G 53 " pdb=" CD GLU C 32 " model vdw 1.352 3.270 nonbonded pdb=" OD2 ASP G 49 " pdb=" CG1 VAL C 68 " model vdw 1.422 3.460 nonbonded pdb=" N GLN G 54 " pdb=" N GLU C 32 " model vdw 1.450 3.200 ... (remaining 152483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 13.580 Check model and map are aligned: 0.210 Set scattering table: 0.160 Process input model: 44.600 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 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 : 0.011 0.080 18456 Z= 0.746 Angle : 1.458 10.725 25141 Z= 0.897 Chirality : 0.092 0.604 2792 Planarity : 0.006 0.055 3245 Dihedral : 15.400 88.397 6583 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.92 % Allowed : 6.03 % Favored : 93.05 % Rotamer: Outliers : 5.13 % Allowed : 10.01 % Favored : 84.87 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % 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: -3.28 (0.15), residues: 2289 helix: -2.98 (0.27), residues: 224 sheet: -2.11 (0.16), residues: 829 loop : -2.02 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP F 144 HIS 0.004 0.002 HIS B 331 PHE 0.028 0.005 PHE E 62 TYR 0.024 0.005 TYR E 105 ARG 0.017 0.002 ARG I 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 526 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.6123 (mtt180) cc_final: 0.5699 (mtt-85) REVERT: B 31 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6439 (tt) REVERT: B 154 SER cc_start: 0.5293 (OUTLIER) cc_final: 0.5021 (t) REVERT: B 225 GLN cc_start: 0.7197 (mm110) cc_final: 0.6385 (tm-30) REVERT: B 245 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 266 ILE cc_start: 0.5985 (mm) cc_final: 0.5777 (mm) REVERT: B 292 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5638 (tp30) REVERT: B 300 SER cc_start: 0.7158 (p) cc_final: 0.6817 (p) REVERT: D 16 ILE cc_start: 0.6667 (mt) cc_final: 0.6233 (mt) REVERT: D 103 TYR cc_start: 0.3206 (m-80) cc_final: -0.0754 (p90) REVERT: E 36 MET cc_start: 0.5994 (ptt) cc_final: 0.5759 (ptt) REVERT: E 154 SER cc_start: 0.4578 (OUTLIER) cc_final: 0.4332 (t) REVERT: E 210 VAL cc_start: 0.6048 (t) cc_final: 0.5402 (t) REVERT: E 225 GLN cc_start: 0.7080 (mm110) cc_final: 0.6346 (tm-30) REVERT: E 245 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: E 352 LYS cc_start: 0.8242 (tttm) cc_final: 0.7928 (tppt) REVERT: E 353 ASP cc_start: 0.7630 (t0) cc_final: 0.7309 (m-30) REVERT: F 16 ILE cc_start: 0.6661 (mt) cc_final: 0.6191 (mt) REVERT: F 71 HIS cc_start: 0.7218 (m-70) cc_final: 0.6936 (m-70) REVERT: F 77 ARG cc_start: 0.5808 (mtt180) cc_final: 0.5322 (tpt170) REVERT: F 82 LYS cc_start: 0.5163 (mttp) cc_final: 0.4960 (tptt) REVERT: F 96 GLN cc_start: 0.7273 (tp40) cc_final: 0.7019 (pm20) REVERT: F 97 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7609 (p) REVERT: G 55 ASP cc_start: 0.6968 (t70) cc_final: 0.6502 (t0) REVERT: G 210 VAL cc_start: 0.6242 (t) cc_final: 0.5623 (t) REVERT: G 225 GLN cc_start: 0.6993 (mm110) cc_final: 0.6350 (tm-30) REVERT: G 245 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: G 292 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6170 (tp30) REVERT: G 294 LYS cc_start: 0.5210 (OUTLIER) cc_final: 0.4852 (tppt) REVERT: G 352 LYS cc_start: 0.8215 (tttm) cc_final: 0.7885 (tppt) REVERT: G 353 ASP cc_start: 0.7660 (t0) cc_final: 0.7347 (m-30) REVERT: H 36 ASN cc_start: 0.6554 (m-40) cc_final: 0.6299 (m110) REVERT: H 71 HIS cc_start: 0.7083 (m-70) cc_final: 0.6515 (m-70) REVERT: H 81 VAL cc_start: 0.4705 (t) cc_final: 0.4457 (t) REVERT: H 103 TYR cc_start: 0.2896 (m-80) cc_final: -0.1077 (p90) REVERT: I 82 ASP cc_start: 0.7112 (p0) cc_final: 0.6816 (m-30) REVERT: I 121 LYS cc_start: 0.6637 (mtmm) cc_final: 0.6411 (tmtt) REVERT: I 154 SER cc_start: 0.5055 (OUTLIER) cc_final: 0.4766 (t) REVERT: I 169 ASP cc_start: 0.8281 (m-30) cc_final: 0.8026 (m-30) REVERT: I 210 VAL cc_start: 0.5767 (t) cc_final: 0.5086 (t) REVERT: I 225 GLN cc_start: 0.7281 (mm110) cc_final: 0.6387 (pp30) REVERT: I 292 GLU cc_start: 0.5864 (OUTLIER) cc_final: 0.5514 (tp30) outliers start: 102 outliers final: 7 residues processed: 591 average time/residue: 0.3205 time to fit residues: 275.0377 Evaluate side-chains 304 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 285 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain G residue 292 GLU Chi-restraints excluded: chain G residue 294 LYS Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 292 GLU Chi-restraints excluded: chain I residue 294 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 71 HIS A 112 GLN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN E 27 GLN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 GLN F 48 ASN F 112 GLN F 128 ASN G 27 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN G 130 ASN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 158 GLN I 27 GLN I 233 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18456 Z= 0.205 Angle : 0.629 7.687 25141 Z= 0.325 Chirality : 0.046 0.178 2792 Planarity : 0.005 0.049 3245 Dihedral : 7.240 70.745 2498 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.75 % Favored : 97.03 % Rotamer: Outliers : 4.12 % Allowed : 17.75 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2289 helix: -1.84 (0.31), residues: 232 sheet: -1.38 (0.18), residues: 756 loop : -1.45 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 47 HIS 0.003 0.001 HIS A 71 PHE 0.015 0.002 PHE G 56 TYR 0.027 0.001 TYR C 75 ARG 0.009 0.001 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 331 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.6373 (m-30) cc_final: 0.6164 (m-30) REVERT: A 128 ASN cc_start: 0.6240 (OUTLIER) cc_final: 0.6019 (m-40) REVERT: B 176 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7330 (tmtt) REVERT: B 225 GLN cc_start: 0.7378 (mm110) cc_final: 0.6528 (tm-30) REVERT: B 245 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: B 352 LYS cc_start: 0.8025 (tttm) cc_final: 0.7721 (tppt) REVERT: D 112 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6533 (tm-30) REVERT: D 141 GLN cc_start: 0.6512 (mt0) cc_final: 0.6136 (mp10) REVERT: E 82 ASP cc_start: 0.7742 (p0) cc_final: 0.6825 (m-30) REVERT: E 100 TYR cc_start: 0.5742 (p90) cc_final: 0.5538 (p90) REVERT: E 174 ASN cc_start: 0.6888 (t0) cc_final: 0.6597 (t0) REVERT: E 176 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7641 (ttmm) REVERT: E 225 GLN cc_start: 0.7204 (mm110) cc_final: 0.6478 (tm-30) REVERT: E 245 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: E 302 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8013 (mp-120) REVERT: E 352 LYS cc_start: 0.8267 (tttm) cc_final: 0.7905 (tppt) REVERT: E 353 ASP cc_start: 0.7425 (t0) cc_final: 0.7176 (m-30) REVERT: E 363 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7286 (mm) REVERT: F 112 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6607 (tm-30) REVERT: F 141 GLN cc_start: 0.6667 (mt0) cc_final: 0.6299 (mp10) REVERT: G 82 ASP cc_start: 0.7700 (p0) cc_final: 0.6789 (m-30) REVERT: G 100 TYR cc_start: 0.5754 (p90) cc_final: 0.5553 (p90) REVERT: G 176 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7628 (ttmm) REVERT: G 225 GLN cc_start: 0.7264 (mm110) cc_final: 0.6344 (tm-30) REVERT: G 245 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: G 352 LYS cc_start: 0.8245 (tttm) cc_final: 0.7836 (tppt) REVERT: G 353 ASP cc_start: 0.7636 (t0) cc_final: 0.7346 (m-30) REVERT: G 363 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7174 (mm) REVERT: I 82 ASP cc_start: 0.7640 (p0) cc_final: 0.7037 (m-30) REVERT: I 100 TYR cc_start: 0.5729 (p90) cc_final: 0.5522 (p90) REVERT: I 121 LYS cc_start: 0.7022 (mtmm) cc_final: 0.6710 (tmtt) REVERT: I 176 LYS cc_start: 0.7030 (mmtt) cc_final: 0.6824 (ttmm) REVERT: I 225 GLN cc_start: 0.7403 (mm110) cc_final: 0.6428 (tm-30) REVERT: I 352 LYS cc_start: 0.7856 (tttm) cc_final: 0.7441 (tppt) REVERT: I 353 ASP cc_start: 0.7596 (t0) cc_final: 0.7318 (m-30) outliers start: 82 outliers final: 33 residues processed: 387 average time/residue: 0.2690 time to fit residues: 165.2053 Evaluate side-chains 293 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 251 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 245 GLU Chi-restraints excluded: chain E residue 302 GLN Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 245 GLU Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 363 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 363 ILE Chi-restraints excluded: chain C residue 32 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 202 optimal weight: 0.9980 chunk 219 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 162 optimal weight: 30.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 112 GLN B 233 ASN E 4 ASN E 27 GLN E 233 ASN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 233 ASN G 331 HIS I 4 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.9025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 18456 Z= 0.497 Angle : 0.880 11.728 25141 Z= 0.459 Chirality : 0.055 0.224 2792 Planarity : 0.007 0.050 3245 Dihedral : 6.903 86.281 2469 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.07 % Favored : 93.71 % Rotamer: Outliers : 5.98 % Allowed : 18.85 % Favored : 75.16 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.16), residues: 2289 helix: -1.71 (0.37), residues: 180 sheet: -1.00 (0.19), residues: 798 loop : -2.06 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP F 47 HIS 0.005 0.001 HIS B 283 PHE 0.027 0.003 PHE I 56 TYR 0.019 0.003 TYR B 325 ARG 0.008 0.001 ARG I 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 233 time to evaluate : 1.817 Fit side-chains REVERT: A 19 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8509 (t) REVERT: A 112 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7821 (tp40) REVERT: A 117 MET cc_start: 0.8784 (mpp) cc_final: 0.8505 (mtm) REVERT: A 143 THR cc_start: 0.8068 (p) cc_final: 0.7841 (t) REVERT: A 160 GLU cc_start: 0.8258 (tt0) cc_final: 0.8036 (tt0) REVERT: A 162 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8405 (m110) REVERT: B 42 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7908 (mm) REVERT: B 51 VAL cc_start: 0.8527 (p) cc_final: 0.8299 (p) REVERT: B 55 ASP cc_start: 0.7812 (t70) cc_final: 0.7096 (t0) REVERT: B 148 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8222 (tmm) REVERT: B 174 ASN cc_start: 0.7760 (t0) cc_final: 0.7189 (t0) REVERT: B 245 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8516 (tt0) REVERT: B 290 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: D 101 GLU cc_start: 0.8445 (mp0) cc_final: 0.6818 (tm-30) REVERT: D 189 LEU cc_start: 0.5756 (pt) cc_final: 0.4702 (tt) REVERT: E 174 ASN cc_start: 0.7615 (t0) cc_final: 0.7150 (t0) REVERT: E 176 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8349 (ttmm) REVERT: E 189 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7969 (m110) REVERT: E 245 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8258 (mp0) REVERT: E 347 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8403 (tttp) REVERT: E 352 LYS cc_start: 0.8814 (tttm) cc_final: 0.8108 (tppt) REVERT: E 353 ASP cc_start: 0.8763 (t0) cc_final: 0.8516 (m-30) REVERT: F 82 LYS cc_start: 0.7453 (mttp) cc_final: 0.6925 (tptt) REVERT: F 104 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: F 132 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8123 (tt0) REVERT: F 189 LEU cc_start: 0.6362 (pt) cc_final: 0.5527 (tt) REVERT: G 99 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8256 (tmtt) REVERT: G 174 ASN cc_start: 0.7619 (t0) cc_final: 0.7363 (t0) REVERT: G 176 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8296 (ttmm) REVERT: G 189 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7941 (m110) REVERT: G 245 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8749 (mt-10) REVERT: G 352 LYS cc_start: 0.8807 (tttm) cc_final: 0.8205 (tppt) REVERT: G 353 ASP cc_start: 0.8701 (t0) cc_final: 0.8408 (m-30) REVERT: H 69 THR cc_start: 0.8461 (m) cc_final: 0.8259 (p) REVERT: H 98 MET cc_start: 0.7807 (tpp) cc_final: 0.7274 (tpp) REVERT: H 101 GLU cc_start: 0.8646 (mp0) cc_final: 0.7161 (tm-30) REVERT: H 117 MET cc_start: 0.8968 (mmm) cc_final: 0.8646 (mmm) REVERT: H 160 GLU cc_start: 0.7946 (tt0) cc_final: 0.7690 (mt-10) REVERT: I 169 ASP cc_start: 0.8758 (m-30) cc_final: 0.8322 (t0) REVERT: I 174 ASN cc_start: 0.7705 (t0) cc_final: 0.7111 (t0) REVERT: I 176 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8157 (ttmm) REVERT: I 189 ASN cc_start: 0.8321 (p0) cc_final: 0.8107 (m110) REVERT: I 245 GLU cc_start: 0.8628 (mp0) cc_final: 0.8413 (mp0) REVERT: I 305 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7970 (t) REVERT: I 353 ASP cc_start: 0.8774 (t0) cc_final: 0.8483 (m-30) outliers start: 119 outliers final: 58 residues processed: 325 average time/residue: 0.2494 time to fit residues: 130.5443 Evaluate side-chains 259 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 189 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 333 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 203 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN F 112 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 119 ASN I 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.9460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18456 Z= 0.220 Angle : 0.570 10.222 25141 Z= 0.286 Chirality : 0.045 0.156 2792 Planarity : 0.005 0.050 3245 Dihedral : 5.132 76.436 2462 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.97 % Favored : 96.85 % Rotamer: Outliers : 4.93 % Allowed : 19.86 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2289 helix: -0.97 (0.40), residues: 180 sheet: -0.78 (0.19), residues: 824 loop : -1.76 (0.15), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 94 HIS 0.003 0.001 HIS G 283 PHE 0.019 0.002 PHE D 165 TYR 0.010 0.001 TYR I 100 ARG 0.004 0.001 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 198 time to evaluate : 1.988 Fit side-chains REVERT: A 15 MET cc_start: 0.8108 (mtm) cc_final: 0.7821 (mtm) REVERT: A 19 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8593 (m) REVERT: A 112 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: A 162 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8210 (m110) REVERT: B 55 ASP cc_start: 0.8004 (t70) cc_final: 0.7230 (t0) REVERT: B 75 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8050 (p) REVERT: B 169 ASP cc_start: 0.8819 (m-30) cc_final: 0.8223 (p0) REVERT: B 174 ASN cc_start: 0.7803 (t0) cc_final: 0.7359 (t0) REVERT: B 245 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: D 101 GLU cc_start: 0.8446 (mp0) cc_final: 0.6868 (tm-30) REVERT: D 104 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: D 112 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7420 (tm-30) REVERT: D 189 LEU cc_start: 0.6216 (pt) cc_final: 0.5319 (tt) REVERT: E 145 ARG cc_start: 0.8333 (mmt90) cc_final: 0.8110 (mmt180) REVERT: E 174 ASN cc_start: 0.7693 (t0) cc_final: 0.7244 (t0) REVERT: E 176 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8337 (ttmm) REVERT: E 189 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7939 (m110) REVERT: E 245 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8734 (mt-10) REVERT: E 352 LYS cc_start: 0.8962 (tttm) cc_final: 0.8329 (tppt) REVERT: E 353 ASP cc_start: 0.8693 (t0) cc_final: 0.8428 (m-30) REVERT: F 82 LYS cc_start: 0.7558 (mtpp) cc_final: 0.7298 (tptt) REVERT: F 189 LEU cc_start: 0.6359 (pt) cc_final: 0.5599 (tt) REVERT: G 99 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8232 (tmtt) REVERT: G 140 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8098 (tpp) REVERT: G 145 ARG cc_start: 0.8197 (mmt90) cc_final: 0.7947 (mmt180) REVERT: G 174 ASN cc_start: 0.7700 (t0) cc_final: 0.7252 (t0) REVERT: G 176 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8320 (ttmm) REVERT: G 189 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7920 (m110) REVERT: G 347 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8360 (tttp) REVERT: G 352 LYS cc_start: 0.8917 (tttm) cc_final: 0.8257 (tppt) REVERT: G 353 ASP cc_start: 0.8762 (t0) cc_final: 0.8495 (m-30) REVERT: H 101 GLU cc_start: 0.8663 (mp0) cc_final: 0.7177 (tm-30) REVERT: H 112 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7413 (tm130) REVERT: I 174 ASN cc_start: 0.8054 (t0) cc_final: 0.7516 (t0) REVERT: I 176 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8249 (ttmm) REVERT: I 213 MET cc_start: 0.8795 (mtm) cc_final: 0.8571 (mtm) REVERT: I 245 GLU cc_start: 0.8588 (mp0) cc_final: 0.8299 (mp0) REVERT: I 249 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8867 (tm-30) REVERT: I 303 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: I 353 ASP cc_start: 0.8882 (t0) cc_final: 0.8630 (m-30) REVERT: I 368 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5753 (mt) outliers start: 98 outliers final: 56 residues processed: 273 average time/residue: 0.2713 time to fit residues: 115.3414 Evaluate side-chains 247 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 178 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 363 ILE Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 1.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 18456 Z= 0.451 Angle : 0.707 13.927 25141 Z= 0.354 Chirality : 0.049 0.255 2792 Planarity : 0.006 0.053 3245 Dihedral : 5.482 83.135 2462 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.71 % Rotamer: Outliers : 5.78 % Allowed : 19.05 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.17), residues: 2289 helix: -2.03 (0.31), residues: 224 sheet: -0.97 (0.18), residues: 878 loop : -1.85 (0.16), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 144 HIS 0.005 0.001 HIS E 283 PHE 0.023 0.003 PHE B 25 TYR 0.016 0.002 TYR D 103 ARG 0.008 0.001 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 188 time to evaluate : 2.116 Fit side-chains REVERT: A 15 MET cc_start: 0.8681 (mtm) cc_final: 0.8455 (mtm) REVERT: A 40 THR cc_start: 0.8190 (m) cc_final: 0.7819 (p) REVERT: B 42 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8168 (mm) REVERT: B 55 ASP cc_start: 0.8394 (t70) cc_final: 0.7609 (t0) REVERT: B 75 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8087 (p) REVERT: B 148 MET cc_start: 0.8869 (ttp) cc_final: 0.8634 (ttp) REVERT: B 169 ASP cc_start: 0.8984 (m-30) cc_final: 0.8453 (p0) REVERT: B 174 ASN cc_start: 0.8390 (t0) cc_final: 0.7812 (t0) REVERT: B 236 ILE cc_start: 0.9093 (tt) cc_final: 0.8771 (tp) REVERT: D 101 GLU cc_start: 0.8698 (mp0) cc_final: 0.7262 (tm-30) REVERT: D 104 ASP cc_start: 0.8828 (m-30) cc_final: 0.8615 (m-30) REVERT: D 189 LEU cc_start: 0.6499 (pt) cc_final: 0.5757 (tt) REVERT: E 99 LYS cc_start: 0.8744 (mmmm) cc_final: 0.8421 (tmtt) REVERT: E 134 ASP cc_start: 0.8841 (p0) cc_final: 0.7912 (t0) REVERT: E 174 ASN cc_start: 0.8300 (t0) cc_final: 0.7718 (t0) REVERT: E 231 MET cc_start: 0.8996 (tmm) cc_final: 0.8759 (tmm) REVERT: E 352 LYS cc_start: 0.9123 (tttm) cc_final: 0.8731 (ttmp) REVERT: E 353 ASP cc_start: 0.8970 (t0) cc_final: 0.8694 (m-30) REVERT: F 189 LEU cc_start: 0.6970 (pt) cc_final: 0.6479 (tt) REVERT: G 99 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8372 (tmtt) REVERT: G 134 ASP cc_start: 0.8799 (p0) cc_final: 0.7893 (t0) REVERT: G 174 ASN cc_start: 0.8317 (t0) cc_final: 0.7710 (t0) REVERT: G 176 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8546 (mttp) REVERT: G 231 MET cc_start: 0.8988 (tmm) cc_final: 0.8752 (tmm) REVERT: G 284 ARG cc_start: 0.6919 (tmt-80) cc_final: 0.6602 (tpt170) REVERT: G 353 ASP cc_start: 0.8950 (t0) cc_final: 0.8658 (m-30) REVERT: H 38 LYS cc_start: 0.7499 (tptp) cc_final: 0.6819 (ttmm) REVERT: H 57 MET cc_start: 0.8640 (tpt) cc_final: 0.8370 (tpt) REVERT: H 70 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8729 (pt) REVERT: H 98 MET cc_start: 0.8187 (tpt) cc_final: 0.7814 (tpp) REVERT: H 101 GLU cc_start: 0.8783 (mp0) cc_final: 0.7332 (tm-30) REVERT: I 100 TYR cc_start: 0.8483 (p90) cc_final: 0.8212 (p90) REVERT: I 111 ASP cc_start: 0.7026 (m-30) cc_final: 0.6810 (m-30) REVERT: I 134 ASP cc_start: 0.9071 (p0) cc_final: 0.8085 (t70) REVERT: I 174 ASN cc_start: 0.8551 (t0) cc_final: 0.7916 (t0) REVERT: I 176 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8471 (mttp) REVERT: I 178 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7381 (pm20) REVERT: I 245 GLU cc_start: 0.8513 (mp0) cc_final: 0.8197 (mp0) REVERT: I 303 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: I 368 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5721 (mt) outliers start: 115 outliers final: 69 residues processed: 280 average time/residue: 0.2843 time to fit residues: 123.9946 Evaluate side-chains 244 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 170 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN D 112 GLN ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN G 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 1.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18456 Z= 0.235 Angle : 0.554 13.116 25141 Z= 0.268 Chirality : 0.044 0.159 2792 Planarity : 0.004 0.055 3245 Dihedral : 4.608 18.572 2459 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.78 % Allowed : 19.76 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.17), residues: 2289 helix: -1.70 (0.32), residues: 228 sheet: -0.78 (0.18), residues: 866 loop : -1.67 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 115 HIS 0.003 0.001 HIS D 71 PHE 0.018 0.002 PHE D 165 TYR 0.011 0.001 TYR D 11 ARG 0.005 0.000 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 183 time to evaluate : 2.070 Fit side-chains REVERT: A 40 THR cc_start: 0.8129 (m) cc_final: 0.7767 (p) REVERT: A 69 THR cc_start: 0.8446 (m) cc_final: 0.8189 (p) REVERT: A 98 MET cc_start: 0.8192 (tpp) cc_final: 0.7969 (mpp) REVERT: B 55 ASP cc_start: 0.8413 (t70) cc_final: 0.7605 (t0) REVERT: B 148 MET cc_start: 0.8912 (ttp) cc_final: 0.8584 (ttp) REVERT: B 174 ASN cc_start: 0.8458 (t0) cc_final: 0.8051 (t0) REVERT: D 101 GLU cc_start: 0.8734 (mp0) cc_final: 0.7272 (tm-30) REVERT: D 189 LEU cc_start: 0.6315 (pt) cc_final: 0.5650 (tt) REVERT: E 99 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8440 (tmtt) REVERT: E 134 ASP cc_start: 0.8859 (p0) cc_final: 0.7870 (t0) REVERT: E 148 MET cc_start: 0.9117 (tmm) cc_final: 0.8333 (ttp) REVERT: E 174 ASN cc_start: 0.8452 (t0) cc_final: 0.7896 (t0) REVERT: E 175 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8807 (mt-10) REVERT: E 352 LYS cc_start: 0.9116 (tttm) cc_final: 0.8678 (ttmp) REVERT: F 189 LEU cc_start: 0.6946 (pt) cc_final: 0.6513 (tt) REVERT: G 89 MET cc_start: 0.8882 (ptm) cc_final: 0.8678 (ttm) REVERT: G 99 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8292 (tmtt) REVERT: G 134 ASP cc_start: 0.8836 (p0) cc_final: 0.7922 (t0) REVERT: G 140 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7911 (tpp) REVERT: G 148 MET cc_start: 0.9027 (tmm) cc_final: 0.8741 (tmm) REVERT: G 174 ASN cc_start: 0.8418 (t0) cc_final: 0.7887 (t0) REVERT: G 290 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7393 (mm-30) REVERT: G 353 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8834 (m-30) REVERT: H 38 LYS cc_start: 0.7592 (tptp) cc_final: 0.7033 (ttmm) REVERT: H 57 MET cc_start: 0.8541 (tpt) cc_final: 0.8249 (tpt) REVERT: H 70 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8660 (pt) REVERT: H 101 GLU cc_start: 0.8789 (mp0) cc_final: 0.7331 (tm-30) REVERT: I 89 MET cc_start: 0.8830 (ttp) cc_final: 0.8513 (ttp) REVERT: I 111 ASP cc_start: 0.6993 (m-30) cc_final: 0.6747 (m-30) REVERT: I 134 ASP cc_start: 0.9078 (p0) cc_final: 0.7994 (t0) REVERT: I 174 ASN cc_start: 0.8590 (t0) cc_final: 0.8072 (t0) REVERT: I 176 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8580 (mttp) REVERT: I 178 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7249 (pm20) REVERT: I 303 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7626 (mp0) outliers start: 95 outliers final: 57 residues processed: 260 average time/residue: 0.2578 time to fit residues: 105.7047 Evaluate side-chains 231 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 170 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 353 ASP Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 303 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 181 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 214 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN E 27 GLN F 112 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 1.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18456 Z= 0.142 Angle : 0.512 12.563 25141 Z= 0.243 Chirality : 0.043 0.159 2792 Planarity : 0.004 0.053 3245 Dihedral : 4.223 17.255 2459 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.77 % Allowed : 20.61 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2289 helix: -1.53 (0.33), residues: 228 sheet: -0.51 (0.20), residues: 826 loop : -1.37 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 156 HIS 0.003 0.000 HIS D 71 PHE 0.016 0.001 PHE D 165 TYR 0.011 0.001 TYR E 100 ARG 0.005 0.000 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 187 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: A 40 THR cc_start: 0.8346 (m) cc_final: 0.7958 (p) REVERT: B 36 MET cc_start: 0.8354 (ptt) cc_final: 0.8093 (ptt) REVERT: B 55 ASP cc_start: 0.8352 (t70) cc_final: 0.7603 (t0) REVERT: B 75 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8197 (p) REVERT: B 148 MET cc_start: 0.8927 (ttp) cc_final: 0.8707 (ttp) REVERT: B 169 ASP cc_start: 0.8845 (m-30) cc_final: 0.8349 (p0) REVERT: B 174 ASN cc_start: 0.8338 (t0) cc_final: 0.7946 (t0) REVERT: B 347 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8363 (tttt) REVERT: D 101 GLU cc_start: 0.8727 (mp0) cc_final: 0.7262 (tm-30) REVERT: D 112 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7764 (tm130) REVERT: D 177 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8973 (mmm) REVERT: D 189 LEU cc_start: 0.6255 (pt) cc_final: 0.5628 (tt) REVERT: E 99 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8396 (tmtt) REVERT: E 134 ASP cc_start: 0.8819 (p0) cc_final: 0.7901 (t0) REVERT: E 148 MET cc_start: 0.9104 (tmm) cc_final: 0.8677 (ttp) REVERT: E 174 ASN cc_start: 0.8428 (t0) cc_final: 0.7947 (t0) REVERT: E 175 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8823 (mt-10) REVERT: E 352 LYS cc_start: 0.9080 (tttm) cc_final: 0.8649 (ttmp) REVERT: F 82 LYS cc_start: 0.3263 (tptt) cc_final: 0.2924 (tptt) REVERT: F 117 MET cc_start: 0.8862 (mpp) cc_final: 0.8443 (mtt) REVERT: F 189 LEU cc_start: 0.7114 (pt) cc_final: 0.6738 (tt) REVERT: G 99 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8368 (tmtt) REVERT: G 134 ASP cc_start: 0.8747 (p0) cc_final: 0.7943 (t0) REVERT: G 140 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7851 (tpp) REVERT: G 174 ASN cc_start: 0.8403 (t0) cc_final: 0.7870 (t0) REVERT: G 353 ASP cc_start: 0.9014 (t0) cc_final: 0.8813 (m-30) REVERT: H 38 LYS cc_start: 0.7760 (tptp) cc_final: 0.7133 (ttmm) REVERT: H 57 MET cc_start: 0.8443 (tpt) cc_final: 0.8167 (tpt) REVERT: H 70 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8564 (pt) REVERT: H 101 GLU cc_start: 0.8782 (mp0) cc_final: 0.7316 (tm-30) REVERT: I 89 MET cc_start: 0.8816 (ttp) cc_final: 0.8527 (ttp) REVERT: I 111 ASP cc_start: 0.6993 (m-30) cc_final: 0.6751 (m-30) REVERT: I 134 ASP cc_start: 0.9105 (p0) cc_final: 0.8042 (t0) REVERT: I 174 ASN cc_start: 0.8552 (t0) cc_final: 0.8025 (t0) REVERT: I 176 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8468 (mttp) REVERT: I 178 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7200 (pm20) REVERT: I 303 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7743 (mp0) outliers start: 75 outliers final: 44 residues processed: 247 average time/residue: 0.2672 time to fit residues: 103.2678 Evaluate side-chains 224 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 173 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 303 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 195 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 1.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18456 Z= 0.265 Angle : 0.568 13.649 25141 Z= 0.269 Chirality : 0.044 0.157 2792 Planarity : 0.004 0.052 3245 Dihedral : 4.337 17.947 2459 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.52 % Allowed : 20.92 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.17), residues: 2289 helix: -1.69 (0.32), residues: 232 sheet: -0.57 (0.20), residues: 802 loop : -1.35 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 144 HIS 0.003 0.001 HIS D 71 PHE 0.017 0.002 PHE A 165 TYR 0.014 0.001 TYR F 145 ARG 0.005 0.000 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 170 time to evaluate : 2.051 Fit side-chains revert: symmetry clash REVERT: A 40 THR cc_start: 0.8450 (m) cc_final: 0.8081 (p) REVERT: A 69 THR cc_start: 0.8482 (m) cc_final: 0.8209 (p) REVERT: B 55 ASP cc_start: 0.8356 (t70) cc_final: 0.7622 (t0) REVERT: B 75 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8242 (p) REVERT: B 88 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8677 (mm) REVERT: B 148 MET cc_start: 0.8960 (ttp) cc_final: 0.8739 (ttp) REVERT: B 169 ASP cc_start: 0.8859 (m-30) cc_final: 0.8388 (p0) REVERT: B 174 ASN cc_start: 0.8492 (t0) cc_final: 0.8096 (t0) REVERT: B 347 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8405 (tttt) REVERT: D 101 GLU cc_start: 0.8718 (mp0) cc_final: 0.7263 (tm-30) REVERT: D 112 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7794 (tm130) REVERT: D 177 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8920 (mmm) REVERT: D 189 LEU cc_start: 0.6356 (pt) cc_final: 0.5771 (tt) REVERT: E 99 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8421 (tmtt) REVERT: E 134 ASP cc_start: 0.8805 (p0) cc_final: 0.7938 (t0) REVERT: E 148 MET cc_start: 0.9128 (tmm) cc_final: 0.8435 (ttp) REVERT: E 174 ASN cc_start: 0.8478 (t0) cc_final: 0.7935 (t0) REVERT: E 175 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8806 (mt-10) REVERT: E 352 LYS cc_start: 0.9081 (tttm) cc_final: 0.8667 (ttmp) REVERT: F 189 LEU cc_start: 0.7153 (pt) cc_final: 0.6846 (tt) REVERT: G 99 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8383 (tmtt) REVERT: G 134 ASP cc_start: 0.8770 (p0) cc_final: 0.7947 (t0) REVERT: G 140 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7826 (tpp) REVERT: G 174 ASN cc_start: 0.8504 (t0) cc_final: 0.7920 (t0) REVERT: H 38 LYS cc_start: 0.7747 (tptp) cc_final: 0.7108 (ttmm) REVERT: H 57 MET cc_start: 0.8477 (tpt) cc_final: 0.8188 (tpt) REVERT: H 101 GLU cc_start: 0.8790 (mp0) cc_final: 0.7344 (tm-30) REVERT: I 89 MET cc_start: 0.8887 (ttp) cc_final: 0.8621 (ttp) REVERT: I 111 ASP cc_start: 0.7104 (m-30) cc_final: 0.6853 (m-30) REVERT: I 134 ASP cc_start: 0.9092 (p0) cc_final: 0.8057 (t0) REVERT: I 174 ASN cc_start: 0.8627 (t0) cc_final: 0.8113 (t0) REVERT: I 228 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8371 (mt) REVERT: I 303 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7803 (mp0) outliers start: 70 outliers final: 55 residues processed: 227 average time/residue: 0.2714 time to fit residues: 97.7227 Evaluate side-chains 228 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 165 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 303 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 1.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18456 Z= 0.221 Angle : 0.545 12.846 25141 Z= 0.257 Chirality : 0.044 0.158 2792 Planarity : 0.004 0.053 3245 Dihedral : 4.302 18.298 2459 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.72 % Allowed : 20.76 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.17), residues: 2289 helix: -1.66 (0.32), residues: 232 sheet: -0.45 (0.20), residues: 798 loop : -1.33 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 196 HIS 0.002 0.001 HIS D 71 PHE 0.017 0.001 PHE F 165 TYR 0.017 0.001 TYR D 145 ARG 0.004 0.000 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 166 time to evaluate : 1.838 Fit side-chains revert: symmetry clash REVERT: A 40 THR cc_start: 0.8374 (m) cc_final: 0.8000 (p) REVERT: B 55 ASP cc_start: 0.8383 (t70) cc_final: 0.7651 (t0) REVERT: B 75 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8228 (p) REVERT: B 88 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8685 (mm) REVERT: B 148 MET cc_start: 0.8935 (ttp) cc_final: 0.8678 (ttp) REVERT: B 169 ASP cc_start: 0.8833 (m-30) cc_final: 0.8381 (p0) REVERT: B 174 ASN cc_start: 0.8488 (t0) cc_final: 0.8113 (t0) REVERT: B 347 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8408 (tttt) REVERT: D 101 GLU cc_start: 0.8659 (mp0) cc_final: 0.7162 (tm-30) REVERT: D 112 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: D 177 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8916 (mmm) REVERT: D 189 LEU cc_start: 0.6487 (pt) cc_final: 0.5937 (tt) REVERT: E 134 ASP cc_start: 0.8780 (p0) cc_final: 0.7938 (t0) REVERT: E 140 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8045 (tpp) REVERT: E 148 MET cc_start: 0.9105 (tmm) cc_final: 0.8419 (ttp) REVERT: E 174 ASN cc_start: 0.8535 (t0) cc_final: 0.8007 (t0) REVERT: E 175 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8803 (mt-10) REVERT: E 352 LYS cc_start: 0.9032 (tttm) cc_final: 0.8631 (ttmp) REVERT: F 117 MET cc_start: 0.8992 (mtm) cc_final: 0.8532 (mtt) REVERT: F 189 LEU cc_start: 0.6985 (pt) cc_final: 0.6703 (tt) REVERT: G 134 ASP cc_start: 0.8761 (p0) cc_final: 0.7910 (t0) REVERT: G 140 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7744 (tpp) REVERT: G 174 ASN cc_start: 0.8542 (t0) cc_final: 0.7956 (t0) REVERT: H 38 LYS cc_start: 0.7861 (tptp) cc_final: 0.7237 (ttmm) REVERT: H 57 MET cc_start: 0.8459 (tpt) cc_final: 0.8197 (tpt) REVERT: H 101 GLU cc_start: 0.8797 (mp0) cc_final: 0.7352 (tm-30) REVERT: I 89 MET cc_start: 0.8885 (ttp) cc_final: 0.8624 (ttp) REVERT: I 96 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8669 (p) REVERT: I 111 ASP cc_start: 0.7102 (m-30) cc_final: 0.6848 (m-30) REVERT: I 134 ASP cc_start: 0.9076 (p0) cc_final: 0.8086 (t0) REVERT: I 174 ASN cc_start: 0.8661 (t0) cc_final: 0.8118 (t0) REVERT: I 178 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7145 (pm20) REVERT: I 228 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8402 (mt) REVERT: I 303 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7822 (mp0) outliers start: 74 outliers final: 57 residues processed: 223 average time/residue: 0.2688 time to fit residues: 95.2537 Evaluate side-chains 230 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 163 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 8.9990 chunk 129 optimal weight: 0.0370 chunk 100 optimal weight: 6.9990 chunk 147 optimal weight: 0.0270 chunk 222 optimal weight: 30.0000 chunk 204 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 overall best weight: 4.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 GLN ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 1.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 18456 Z= 0.386 Angle : 0.637 14.811 25141 Z= 0.306 Chirality : 0.047 0.166 2792 Planarity : 0.005 0.053 3245 Dihedral : 4.683 19.568 2459 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.72 % Allowed : 20.61 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 2289 helix: -1.89 (0.31), residues: 224 sheet: -0.51 (0.19), residues: 836 loop : -1.54 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 235 HIS 0.004 0.001 HIS E 283 PHE 0.021 0.002 PHE B 25 TYR 0.012 0.002 TYR H 93 ARG 0.005 0.001 ARG F 164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 166 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: A 36 ASN cc_start: 0.8685 (m-40) cc_final: 0.8461 (m-40) REVERT: B 55 ASP cc_start: 0.8409 (t70) cc_final: 0.7704 (t0) REVERT: B 75 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8255 (p) REVERT: B 88 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8761 (mm) REVERT: B 148 MET cc_start: 0.8954 (ttp) cc_final: 0.8650 (ttp) REVERT: B 169 ASP cc_start: 0.8835 (m-30) cc_final: 0.8372 (p0) REVERT: B 174 ASN cc_start: 0.8633 (t0) cc_final: 0.8178 (t0) REVERT: D 101 GLU cc_start: 0.8732 (mp0) cc_final: 0.7298 (tm-30) REVERT: D 112 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: D 189 LEU cc_start: 0.6899 (pt) cc_final: 0.6430 (tt) REVERT: E 134 ASP cc_start: 0.8855 (p0) cc_final: 0.8027 (t0) REVERT: E 140 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8160 (tpp) REVERT: E 148 MET cc_start: 0.9098 (tmm) cc_final: 0.8420 (ttp) REVERT: E 174 ASN cc_start: 0.8621 (t0) cc_final: 0.8082 (t0) REVERT: E 175 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8889 (mt-10) REVERT: E 352 LYS cc_start: 0.8913 (tttm) cc_final: 0.8527 (tttp) REVERT: F 6 GLU cc_start: 0.7103 (tt0) cc_final: 0.6663 (tp30) REVERT: F 117 MET cc_start: 0.9027 (mtm) cc_final: 0.8637 (mtt) REVERT: F 189 LEU cc_start: 0.6879 (pt) cc_final: 0.6642 (tt) REVERT: G 134 ASP cc_start: 0.8839 (p0) cc_final: 0.8014 (t0) REVERT: G 140 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.7931 (tpp) REVERT: G 174 ASN cc_start: 0.8672 (t0) cc_final: 0.8098 (t0) REVERT: G 175 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8880 (mt-10) REVERT: H 38 LYS cc_start: 0.7911 (tptp) cc_final: 0.7299 (ttmm) REVERT: H 57 MET cc_start: 0.8531 (tpt) cc_final: 0.8286 (tpt) REVERT: H 101 GLU cc_start: 0.8816 (mp0) cc_final: 0.7435 (tm-30) REVERT: H 189 LEU cc_start: 0.7474 (tt) cc_final: 0.7022 (mp) REVERT: I 89 MET cc_start: 0.8916 (ttp) cc_final: 0.8682 (ttp) REVERT: I 111 ASP cc_start: 0.7216 (m-30) cc_final: 0.6991 (m-30) REVERT: I 134 ASP cc_start: 0.9128 (p0) cc_final: 0.8088 (t70) REVERT: I 174 ASN cc_start: 0.8752 (t0) cc_final: 0.8146 (t0) REVERT: I 178 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7202 (pm20) REVERT: I 228 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8600 (mt) REVERT: I 303 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7747 (mp0) outliers start: 74 outliers final: 56 residues processed: 224 average time/residue: 0.2725 time to fit residues: 96.6941 Evaluate side-chains 225 residues out of total 1989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 162 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 253 MET Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 chunk 155 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 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 = 0.3357 r_free = 0.3357 target = 0.090446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075378 restraints weight = 37159.313| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.20 r_work: 0.2970 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 1.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18456 Z= 0.185 Angle : 0.536 12.423 25141 Z= 0.252 Chirality : 0.043 0.160 2792 Planarity : 0.004 0.054 3245 Dihedral : 4.379 18.511 2459 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.12 % Allowed : 21.32 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2289 helix: -1.76 (0.32), residues: 228 sheet: -0.40 (0.19), residues: 848 loop : -1.45 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 156 HIS 0.002 0.001 HIS D 71 PHE 0.015 0.001 PHE F 165 TYR 0.013 0.001 TYR A 145 ARG 0.003 0.000 ARG D 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4011.34 seconds wall clock time: 73 minutes 9.51 seconds (4389.51 seconds total)