Starting phenix.real_space_refine on Thu Sep 18 16:34:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qoz_4610/09_2025/6qoz_4610.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qoz_4610/09_2025/6qoz_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 { model { file = "/net/cci-nas-00/data/ceres_data/6qoz_4610/09_2025/6qoz_4610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qoz_4610/09_2025/6qoz_4610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qoz_4610/09_2025/6qoz_4610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qoz_4610/09_2025/6qoz_4610.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17987 Number of models: 1 Model: "" Number of chains: 3 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: "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} Restraints were copied for chains: D, F, H, E, G, I Time building chain proxies: 3.15, per 1000 atoms: 0.18 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 551.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.40 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: 1.76 Time building geometry restraints manager: 1.43 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: 0.00 - 2.14: 22217 2.14 - 4.29: 2565 4.29 - 6.43: 261 6.43 - 8.58: 66 8.58 - 10.72: 32 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: 20 1.97 - 2.71: 589 2.71 - 3.44: 24257 3.44 - 4.17: 46687 4.17 - 4.90: 80930 Nonbonded interactions: 152483 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 152478 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 5.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.770 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- 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 0.106 18457 Z= 0.729 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.002 ARG I 145 TYR 0.024 0.005 TYR E 105 PHE 0.028 0.005 PHE E 62 TRP 0.022 0.004 TRP F 144 HIS 0.004 0.002 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.01126 (18456) covalent geometry : angle 1.45757 (25141) hydrogen bonds : bond 0.32843 ( 135) hydrogen bonds : angle 7.41798 ( 273) Misc. bond : bond 0.10558 ( 1) *********************** 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 to be fit. rotamer outliers: 102 poor density : 526 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.6123 (mtt180) cc_final: 0.5696 (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: 0.5020 (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: 0.5639 (tp30) REVERT: B 300 SER cc_start: 0.7158 (p) cc_final: 0.6818 (p) REVERT: D 16 ILE cc_start: 0.6667 (mt) cc_final: 0.6235 (mt) REVERT: D 103 TYR cc_start: 0.3206 (m-80) cc_final: -0.0755 (p90) REVERT: E 36 MET cc_start: 0.5994 (ptt) cc_final: 0.5758 (ptt) REVERT: E 104 VAL cc_start: 0.6737 (p) cc_final: 0.6536 (p) REVERT: E 154 SER cc_start: 0.4578 (OUTLIER) cc_final: 0.4334 (t) REVERT: E 210 VAL cc_start: 0.6048 (t) cc_final: 0.5401 (t) REVERT: E 225 GLN cc_start: 0.7080 (mm110) cc_final: 0.6347 (tm-30) REVERT: E 245 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: E 352 LYS cc_start: 0.8242 (tttm) cc_final: 0.7929 (tppt) REVERT: E 353 ASP cc_start: 0.7630 (t0) cc_final: 0.7308 (m-30) REVERT: F 16 ILE cc_start: 0.6661 (mt) cc_final: 0.6203 (mt) REVERT: F 71 HIS cc_start: 0.7218 (m-70) cc_final: 0.6941 (m-70) REVERT: F 77 ARG cc_start: 0.5808 (mtt180) cc_final: 0.5331 (tpt170) REVERT: F 82 LYS cc_start: 0.5163 (mttp) cc_final: 0.4960 (tptt) 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: 0.6351 (tm-30) REVERT: G 245 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7275 (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: 0.7886 (tppt) REVERT: G 353 ASP cc_start: 0.7660 (t0) cc_final: 0.7346 (m-30) REVERT: H 38 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6771 (tptp) REVERT: H 71 HIS cc_start: 0.7083 (m-70) cc_final: 0.6518 (m-70) REVERT: H 81 VAL cc_start: 0.4705 (t) cc_final: 0.4456 (t) REVERT: H 103 TYR cc_start: 0.2896 (m-80) cc_final: -0.1076 (p90) REVERT: I 82 ASP cc_start: 0.7112 (p0) cc_final: 0.6817 (m-30) REVERT: I 121 LYS cc_start: 0.6637 (mtmm) cc_final: 0.6413 (tmtt) REVERT: I 154 SER cc_start: 0.5055 (OUTLIER) cc_final: 0.4768 (t) REVERT: I 169 ASP cc_start: 0.8281 (m-30) cc_final: 0.8027 (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: 0.6390 (pp30) REVERT: I 292 GLU cc_start: 0.5864 (OUTLIER) cc_final: 0.5512 (tp30) outliers start: 102 outliers final: 7 residues processed: 591 average time/residue: 0.1345 time to fit residues: 116.0747 Evaluate side-chains 306 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 287 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 H residue 38 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 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS B 122 ASN B 233 ASN D 73 GLN D 112 GLN E 27 GLN E 233 ASN E 302 GLN E 311 GLN F 48 ASN F 112 GLN G 27 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 GLN H 48 ASN H 158 GLN I 27 GLN I 233 ASN I 311 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.108097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093372 restraints weight = 36094.026| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.20 r_work: 0.3326 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 18457 Z= 0.206 Angle : 0.726 8.157 25141 Z= 0.379 Chirality : 0.049 0.229 2792 Planarity : 0.006 0.052 3245 Dihedral : 7.329 74.770 2501 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.23 % Favored : 96.59 % Rotamer: Outliers : 3.67 % Allowed : 17.04 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.16), residues: 2289 helix: -1.69 (0.34), residues: 208 sheet: -1.54 (0.18), residues: 751 loop : -1.48 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 17 TYR 0.030 0.002 TYR C 75 PHE 0.029 0.003 PHE G 56 TRP 0.031 0.003 TRP D 47 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00472 (18456) covalent geometry : angle 0.72604 (25141) hydrogen bonds : bond 0.04539 ( 135) hydrogen bonds : angle 5.43196 ( 273) Misc. bond : bond 0.01472 ( 1) *********************** 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 397 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 324 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 225 GLN cc_start: 0.7402 (mm110) cc_final: 0.6658 (tm-30) REVERT: B 352 LYS cc_start: 0.8671 (tttm) cc_final: 0.8436 (tppt) REVERT: D 138 TRP cc_start: 0.7025 (t-100) cc_final: 0.6786 (t-100) REVERT: D 141 GLN cc_start: 0.7315 (mt0) cc_final: 0.7032 (mp10) REVERT: E 69 THR cc_start: 0.7972 (p) cc_final: 0.7714 (m) REVERT: E 82 ASP cc_start: 0.7439 (p0) cc_final: 0.6895 (m-30) REVERT: E 225 GLN cc_start: 0.7528 (mm110) cc_final: 0.6667 (tm-30) REVERT: E 302 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8027 (mp-120) REVERT: E 348 LEU cc_start: 0.8221 (tt) cc_final: 0.7970 (tp) REVERT: E 352 LYS cc_start: 0.8606 (tttm) cc_final: 0.8355 (tppt) REVERT: E 363 ILE cc_start: 0.7662 (mt) cc_final: 0.7320 (mm) REVERT: F 141 GLN cc_start: 0.7228 (mt0) cc_final: 0.6914 (mp10) REVERT: G 69 THR cc_start: 0.7892 (p) cc_final: 0.7612 (m) REVERT: G 82 ASP cc_start: 0.7632 (p0) cc_final: 0.7040 (m-30) REVERT: G 225 GLN cc_start: 0.7342 (mm110) cc_final: 0.6548 (tm-30) REVERT: G 348 LEU cc_start: 0.8302 (tt) cc_final: 0.8023 (tp) REVERT: G 352 LYS cc_start: 0.8671 (tttm) cc_final: 0.8374 (tppt) REVERT: I 82 ASP cc_start: 0.7498 (p0) cc_final: 0.7156 (m-30) REVERT: I 113 MET cc_start: 0.6927 (ptt) cc_final: 0.6406 (ptt) REVERT: I 169 ASP cc_start: 0.7880 (m-30) cc_final: 0.7548 (m-30) REVERT: I 225 GLN cc_start: 0.7738 (mm110) cc_final: 0.6945 (tm-30) outliers start: 73 outliers final: 34 residues processed: 371 average time/residue: 0.1086 time to fit residues: 63.7668 Evaluate side-chains 268 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 312 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 189 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 77 THR Chi-restraints excluded: chain E residue 302 GLN Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 189 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 77 THR Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain H residue 12 SER 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 329 ILE Chi-restraints excluded: chain I residue 363 ILE Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 3 optimal weight: 0.3980 chunk 141 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 GLN D 112 GLN D 174 ASN E 4 ASN E 302 GLN E 311 GLN F 112 GLN F 174 ASN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 GLN I 4 ASN I 311 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.103314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088630 restraints weight = 36418.757| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.17 r_work: 0.3255 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 18457 Z= 0.148 Angle : 0.624 10.209 25141 Z= 0.319 Chirality : 0.046 0.219 2792 Planarity : 0.005 0.062 3245 Dihedral : 4.753 20.321 2459 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 3.72 % Allowed : 18.70 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.17), residues: 2289 helix: -1.33 (0.37), residues: 204 sheet: -0.67 (0.20), residues: 716 loop : -1.51 (0.15), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 17 TYR 0.015 0.001 TYR C 75 PHE 0.022 0.002 PHE F 131 TRP 0.036 0.002 TRP A 47 HIS 0.003 0.001 HIS D 71 Details of bonding type rmsd covalent geometry : bond 0.00342 (18456) covalent geometry : angle 0.62401 (25141) hydrogen bonds : bond 0.04012 ( 135) hydrogen bonds : angle 4.98995 ( 273) Misc. bond : bond 0.00348 ( 1) *********************** 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 326 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 252 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.7552 (ttm) cc_final: 0.7288 (ttm) REVERT: B 82 ASP cc_start: 0.8088 (p0) cc_final: 0.7289 (m-30) REVERT: B 124 SER cc_start: 0.8155 (t) cc_final: 0.7660 (p) REVERT: B 174 ASN cc_start: 0.7038 (t0) cc_final: 0.6363 (t0) REVERT: B 352 LYS cc_start: 0.8672 (tttm) cc_final: 0.8441 (tppt) REVERT: D 9 ASP cc_start: 0.5243 (m-30) cc_final: 0.4976 (m-30) REVERT: D 112 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: E 82 ASP cc_start: 0.7747 (p0) cc_final: 0.7057 (m-30) REVERT: E 89 MET cc_start: 0.6514 (ptm) cc_final: 0.6306 (ptp) REVERT: E 174 ASN cc_start: 0.7159 (t0) cc_final: 0.6492 (t0) REVERT: E 225 GLN cc_start: 0.7944 (mm110) cc_final: 0.7310 (tm-30) REVERT: E 352 LYS cc_start: 0.8593 (tttm) cc_final: 0.8326 (tppt) REVERT: G 82 ASP cc_start: 0.7946 (p0) cc_final: 0.7300 (m-30) REVERT: G 169 ASP cc_start: 0.8044 (m-30) cc_final: 0.7796 (m-30) REVERT: G 174 ASN cc_start: 0.7101 (t0) cc_final: 0.6384 (t0) REVERT: G 225 GLN cc_start: 0.7804 (mm110) cc_final: 0.7244 (tm-30) REVERT: G 245 GLU cc_start: 0.8376 (mp0) cc_final: 0.8137 (mp0) REVERT: G 352 LYS cc_start: 0.8688 (tttm) cc_final: 0.8370 (tppt) REVERT: H 98 MET cc_start: 0.7842 (tpp) cc_final: 0.7552 (tpp) REVERT: H 117 MET cc_start: 0.8299 (mpp) cc_final: 0.8015 (mmm) REVERT: I 82 ASP cc_start: 0.7978 (p0) cc_final: 0.7336 (m-30) REVERT: I 113 MET cc_start: 0.7976 (ptt) cc_final: 0.7508 (ptt) REVERT: I 169 ASP cc_start: 0.8279 (m-30) cc_final: 0.7986 (m-30) REVERT: I 174 ASN cc_start: 0.7180 (t0) cc_final: 0.6917 (t0) REVERT: I 225 GLN cc_start: 0.8084 (mm110) cc_final: 0.7250 (tm-30) outliers start: 74 outliers final: 33 residues processed: 294 average time/residue: 0.1067 time to fit residues: 50.8272 Evaluate side-chains 259 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain G residue 302 GLN Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 363 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN F 99 ASN F 128 ASN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 ASN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN G 233 ASN H 119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088787 restraints weight = 35583.006| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.92 r_work: 0.3291 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.9890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 18457 Z= 0.248 Angle : 0.743 21.564 25141 Z= 0.382 Chirality : 0.051 0.478 2792 Planarity : 0.006 0.072 3245 Dihedral : 5.311 24.197 2459 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.06 % Favored : 95.72 % Rotamer: Outliers : 5.53 % Allowed : 18.05 % Favored : 76.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.17), residues: 2289 helix: -1.65 (0.37), residues: 180 sheet: -0.93 (0.19), residues: 818 loop : -1.64 (0.15), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 170 TYR 0.016 0.002 TYR B 325 PHE 0.023 0.002 PHE F 131 TRP 0.042 0.002 TRP F 47 HIS 0.006 0.002 HIS I 247 Details of bonding type rmsd covalent geometry : bond 0.00591 (18456) covalent geometry : angle 0.74292 (25141) hydrogen bonds : bond 0.04611 ( 135) hydrogen bonds : angle 5.66111 ( 273) Misc. bond : bond 0.00422 ( 1) *********************** 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 342 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 232 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8992 (mpp) cc_final: 0.8726 (mtm) REVERT: A 143 THR cc_start: 0.8116 (p) cc_final: 0.7858 (t) REVERT: A 189 LEU cc_start: 0.6728 (pt) cc_final: 0.6336 (tt) REVERT: B 1 MET cc_start: 0.7598 (ppp) cc_final: 0.7340 (ppp) REVERT: B 51 VAL cc_start: 0.8875 (p) cc_final: 0.8570 (p) REVERT: B 75 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.7993 (p) REVERT: B 174 ASN cc_start: 0.7726 (t0) cc_final: 0.7167 (t0) REVERT: B 290 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6334 (mp0) REVERT: D 40 THR cc_start: 0.8251 (m) cc_final: 0.7623 (p) REVERT: D 101 GLU cc_start: 0.8414 (mp0) cc_final: 0.7455 (tm-30) REVERT: D 104 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: E 134 ASP cc_start: 0.8025 (p0) cc_final: 0.7749 (t0) REVERT: E 174 ASN cc_start: 0.8071 (t0) cc_final: 0.7604 (t0) REVERT: E 302 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: G 174 ASN cc_start: 0.8039 (t0) cc_final: 0.7483 (t0) REVERT: G 352 LYS cc_start: 0.9179 (tttm) cc_final: 0.8945 (ttmm) REVERT: H 42 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7797 (t) REVERT: H 101 GLU cc_start: 0.8756 (mp0) cc_final: 0.7794 (tm-30) REVERT: H 112 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7896 (tm-30) REVERT: H 160 GLU cc_start: 0.7838 (tt0) cc_final: 0.7576 (tt0) REVERT: H 189 LEU cc_start: 0.6420 (tt) cc_final: 0.6050 (mp) REVERT: I 113 MET cc_start: 0.9203 (ptt) cc_final: 0.8967 (ptt) REVERT: I 169 ASP cc_start: 0.8091 (m-30) cc_final: 0.7794 (m-30) REVERT: I 174 ASN cc_start: 0.8206 (t0) cc_final: 0.7618 (t0) REVERT: I 225 GLN cc_start: 0.8137 (mm110) cc_final: 0.7716 (tm-30) REVERT: I 293 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: I 303 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7458 (mp0) outliers start: 110 outliers final: 50 residues processed: 313 average time/residue: 0.1291 time to fit residues: 62.8337 Evaluate side-chains 246 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 92 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 125 ILE 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 302 GLN Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 69 THR 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 153 VAL Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 VAL 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 H residue 148 CYS Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 69 THR 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 293 GLU Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 333 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 71 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.078538 restraints weight = 36878.645| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.10 r_work: 0.3067 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 1.0198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18457 Z= 0.152 Angle : 0.573 10.301 25141 Z= 0.286 Chirality : 0.045 0.151 2792 Planarity : 0.005 0.064 3245 Dihedral : 4.645 20.171 2459 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.15 % Favored : 96.68 % Rotamer: Outliers : 3.92 % Allowed : 19.66 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.17), residues: 2289 helix: -1.24 (0.39), residues: 180 sheet: -0.62 (0.19), residues: 810 loop : -1.45 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 170 TYR 0.014 0.001 TYR D 11 PHE 0.016 0.002 PHE B 25 TRP 0.013 0.001 TRP A 144 HIS 0.002 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00370 (18456) covalent geometry : angle 0.57290 (25141) hydrogen bonds : bond 0.03302 ( 135) hydrogen bonds : angle 5.20457 ( 273) Misc. bond : bond 0.00059 ( 1) *********************** 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 272 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 194 time to evaluate : 0.703 Fit side-chains REVERT: A 19 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8970 (m) REVERT: A 40 THR cc_start: 0.8371 (m) cc_final: 0.7926 (p) REVERT: A 117 MET cc_start: 0.9030 (mpp) cc_final: 0.8769 (mtm) REVERT: A 143 THR cc_start: 0.8092 (p) cc_final: 0.7850 (t) REVERT: B 1 MET cc_start: 0.7719 (ppp) cc_final: 0.7223 (ptm) REVERT: B 55 ASP cc_start: 0.7905 (t70) cc_final: 0.7168 (t0) REVERT: B 174 ASN cc_start: 0.7939 (t0) cc_final: 0.7442 (t0) REVERT: B 197 MET cc_start: 0.9001 (tpt) cc_final: 0.8766 (tpt) REVERT: D 101 GLU cc_start: 0.8614 (mp0) cc_final: 0.7420 (tm-30) REVERT: E 36 MET cc_start: 0.8330 (ptt) cc_final: 0.8006 (ptt) REVERT: E 134 ASP cc_start: 0.8098 (p0) cc_final: 0.7318 (t0) REVERT: E 148 MET cc_start: 0.9164 (tmm) cc_final: 0.8876 (tmm) REVERT: E 174 ASN cc_start: 0.8138 (t0) cc_final: 0.7591 (t0) REVERT: F 15 MET cc_start: 0.8643 (mtm) cc_final: 0.8436 (mtm) REVERT: F 104 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8175 (m-30) REVERT: F 117 MET cc_start: 0.8699 (mpp) cc_final: 0.8150 (mtt) REVERT: F 148 CYS cc_start: 0.8318 (p) cc_final: 0.8105 (p) REVERT: G 148 MET cc_start: 0.8935 (tmm) cc_final: 0.8687 (tmm) REVERT: G 174 ASN cc_start: 0.8073 (t0) cc_final: 0.7520 (t0) REVERT: G 245 GLU cc_start: 0.8461 (mp0) cc_final: 0.8216 (mp0) REVERT: H 98 MET cc_start: 0.8038 (tpt) cc_final: 0.7642 (tpp) REVERT: H 101 GLU cc_start: 0.8872 (mp0) cc_final: 0.7679 (tm-30) REVERT: H 112 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: H 160 GLU cc_start: 0.8031 (tt0) cc_final: 0.7685 (tt0) REVERT: H 189 LEU cc_start: 0.6649 (tt) cc_final: 0.6264 (mp) REVERT: I 89 MET cc_start: 0.8785 (ttp) cc_final: 0.8521 (ttp) REVERT: I 169 ASP cc_start: 0.8301 (m-30) cc_final: 0.7968 (m-30) REVERT: I 174 ASN cc_start: 0.8327 (t0) cc_final: 0.7756 (t0) REVERT: I 303 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7420 (mp0) outliers start: 78 outliers final: 51 residues processed: 255 average time/residue: 0.1147 time to fit residues: 47.1324 Evaluate side-chains 232 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 177 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR 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 92 VAL Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 215 LEU 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 357 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 69 THR 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 357 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain G residue 20 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 96 VAL Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 363 ILE Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 363 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 114 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 211 optimal weight: 0.4980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 73 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077595 restraints weight = 36922.638| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.29 r_work: 0.3029 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 1.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18457 Z= 0.114 Angle : 0.536 13.552 25141 Z= 0.261 Chirality : 0.044 0.155 2792 Planarity : 0.004 0.063 3245 Dihedral : 4.274 18.403 2459 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.97 % Allowed : 19.56 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.17), residues: 2289 helix: -1.31 (0.37), residues: 204 sheet: -0.43 (0.20), residues: 774 loop : -1.42 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 212 TYR 0.016 0.001 TYR C 75 PHE 0.016 0.001 PHE D 32 TRP 0.010 0.001 TRP A 144 HIS 0.002 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00275 (18456) covalent geometry : angle 0.53584 (25141) hydrogen bonds : bond 0.02882 ( 135) hydrogen bonds : angle 4.94690 ( 273) Misc. bond : bond 0.00195 ( 1) *********************** 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 268 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 189 time to evaluate : 0.502 Fit side-chains REVERT: A 40 THR cc_start: 0.8418 (m) cc_final: 0.8017 (p) REVERT: A 98 MET cc_start: 0.8110 (tpp) cc_final: 0.7771 (mpp) REVERT: A 143 THR cc_start: 0.8069 (p) cc_final: 0.7809 (t) REVERT: B 1 MET cc_start: 0.7592 (ppp) cc_final: 0.7194 (ptm) REVERT: B 36 MET cc_start: 0.8624 (ptt) cc_final: 0.8228 (ptt) REVERT: B 55 ASP cc_start: 0.8111 (t70) cc_final: 0.7378 (t0) REVERT: B 174 ASN cc_start: 0.8082 (t0) cc_final: 0.7575 (t0) REVERT: B 197 MET cc_start: 0.9129 (tpt) cc_final: 0.8913 (tpt) REVERT: D 56 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8220 (mp) REVERT: D 101 GLU cc_start: 0.8700 (mp0) cc_final: 0.7370 (tm-30) REVERT: E 134 ASP cc_start: 0.8182 (p0) cc_final: 0.7559 (t0) REVERT: E 148 MET cc_start: 0.9215 (tmm) cc_final: 0.8961 (tmm) REVERT: E 174 ASN cc_start: 0.8242 (t0) cc_final: 0.7743 (t0) REVERT: F 9 ASP cc_start: 0.6175 (p0) cc_final: 0.5961 (p0) REVERT: F 56 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8121 (mp) REVERT: F 101 GLU cc_start: 0.9059 (mp0) cc_final: 0.8854 (mp0) REVERT: F 104 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8200 (m-30) REVERT: F 117 MET cc_start: 0.8745 (mpp) cc_final: 0.8253 (mtt) REVERT: F 148 CYS cc_start: 0.8402 (p) cc_final: 0.8174 (p) REVERT: F 175 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8770 (pt) REVERT: G 148 MET cc_start: 0.9074 (tmm) cc_final: 0.8851 (tmm) REVERT: G 174 ASN cc_start: 0.8254 (t0) cc_final: 0.7687 (t0) REVERT: G 245 GLU cc_start: 0.8421 (mp0) cc_final: 0.8153 (mp0) REVERT: H 40 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8653 (p) REVERT: H 70 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8812 (pt) REVERT: H 101 GLU cc_start: 0.8931 (mp0) cc_final: 0.7620 (tm-30) REVERT: H 112 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7891 (tt0) REVERT: H 160 GLU cc_start: 0.7951 (tt0) cc_final: 0.7699 (tt0) REVERT: I 89 MET cc_start: 0.8855 (ttp) cc_final: 0.8522 (ttp) REVERT: I 100 TYR cc_start: 0.8625 (p90) cc_final: 0.8342 (p90) REVERT: I 169 ASP cc_start: 0.8349 (m-30) cc_final: 0.7941 (m-30) REVERT: I 174 ASN cc_start: 0.8440 (t0) cc_final: 0.7900 (t0) outliers start: 79 outliers final: 47 residues processed: 251 average time/residue: 0.1252 time to fit residues: 49.0128 Evaluate side-chains 224 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 69 THR 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 153 VAL Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 69 THR 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 96 VAL Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 333 SER Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 363 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 42 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 151 optimal weight: 0.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.091506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076394 restraints weight = 37336.254| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.24 r_work: 0.3000 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 1.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18457 Z= 0.140 Angle : 0.566 14.038 25141 Z= 0.270 Chirality : 0.044 0.152 2792 Planarity : 0.004 0.064 3245 Dihedral : 4.262 18.298 2459 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.82 % Allowed : 19.16 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.17), residues: 2289 helix: -1.57 (0.33), residues: 224 sheet: -0.42 (0.20), residues: 812 loop : -1.43 (0.16), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 164 TYR 0.011 0.001 TYR A 11 PHE 0.019 0.001 PHE A 165 TRP 0.009 0.001 TRP I 115 HIS 0.003 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00345 (18456) covalent geometry : angle 0.56564 (25141) hydrogen bonds : bond 0.03159 ( 135) hydrogen bonds : angle 4.95219 ( 273) Misc. bond : bond 0.00170 ( 1) *********************** 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 252 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 176 time to evaluate : 0.697 Fit side-chains REVERT: A 40 THR cc_start: 0.8561 (m) cc_final: 0.8198 (p) REVERT: A 98 MET cc_start: 0.8085 (tpp) cc_final: 0.7768 (mpp) REVERT: A 135 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7918 (mm-30) REVERT: B 55 ASP cc_start: 0.8169 (t70) cc_final: 0.7449 (t0) REVERT: B 174 ASN cc_start: 0.8211 (t0) cc_final: 0.7648 (t0) REVERT: B 253 MET cc_start: 0.8634 (tpp) cc_final: 0.8000 (mmt) REVERT: D 56 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8304 (mp) REVERT: D 101 GLU cc_start: 0.8723 (mp0) cc_final: 0.7477 (tm-30) REVERT: D 117 MET cc_start: 0.8981 (mpp) cc_final: 0.8626 (mtt) REVERT: D 175 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8886 (pt) REVERT: E 89 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8626 (ttm) REVERT: E 134 ASP cc_start: 0.8232 (p0) cc_final: 0.7637 (t0) REVERT: E 148 MET cc_start: 0.9199 (tmm) cc_final: 0.8935 (tmm) REVERT: E 174 ASN cc_start: 0.8424 (t0) cc_final: 0.7873 (t0) REVERT: F 56 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8450 (mp) REVERT: F 117 MET cc_start: 0.8837 (mpp) cc_final: 0.8322 (mtt) REVERT: G 134 ASP cc_start: 0.8218 (p0) cc_final: 0.7603 (t0) REVERT: G 148 MET cc_start: 0.8984 (tmm) cc_final: 0.8737 (tmm) REVERT: G 174 ASN cc_start: 0.8410 (t0) cc_final: 0.7815 (t0) REVERT: G 245 GLU cc_start: 0.8389 (mp0) cc_final: 0.8088 (mp0) REVERT: H 40 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8743 (p) REVERT: H 70 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8877 (pt) REVERT: H 101 GLU cc_start: 0.8908 (mp0) cc_final: 0.7658 (tm-30) REVERT: H 112 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: H 160 GLU cc_start: 0.7997 (tt0) cc_final: 0.7780 (tt0) REVERT: H 163 MET cc_start: 0.9158 (mtt) cc_final: 0.8871 (mtt) REVERT: H 189 LEU cc_start: 0.7154 (tt) cc_final: 0.6768 (mp) REVERT: I 75 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.7757 (p) REVERT: I 89 MET cc_start: 0.9031 (ttp) cc_final: 0.8750 (ttp) REVERT: I 100 TYR cc_start: 0.8642 (p90) cc_final: 0.8354 (p90) REVERT: I 111 ASP cc_start: 0.6688 (m-30) cc_final: 0.6416 (m-30) REVERT: I 134 ASP cc_start: 0.8562 (p0) cc_final: 0.7841 (t70) REVERT: I 164 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8577 (t) REVERT: I 169 ASP cc_start: 0.8297 (m-30) cc_final: 0.7706 (p0) REVERT: I 174 ASN cc_start: 0.8628 (t0) cc_final: 0.8059 (t0) REVERT: I 245 GLU cc_start: 0.8453 (mp0) cc_final: 0.8154 (mp0) outliers start: 76 outliers final: 49 residues processed: 238 average time/residue: 0.1224 time to fit residues: 45.7032 Evaluate side-chains 223 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 249 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 357 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 175 ILE 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 89 MET Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain G residue 20 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 153 VAL Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain C residue 68 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 163 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 162 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077595 restraints weight = 37034.819| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.28 r_work: 0.3013 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 1.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18457 Z= 0.104 Angle : 0.543 13.942 25141 Z= 0.257 Chirality : 0.043 0.153 2792 Planarity : 0.004 0.064 3245 Dihedral : 4.134 17.698 2459 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.12 % Allowed : 20.16 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.17), residues: 2289 helix: -1.53 (0.34), residues: 224 sheet: -0.30 (0.20), residues: 812 loop : -1.35 (0.16), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 164 TYR 0.012 0.001 TYR D 145 PHE 0.012 0.001 PHE A 165 TRP 0.009 0.001 TRP E 156 HIS 0.002 0.001 HIS H 71 Details of bonding type rmsd covalent geometry : bond 0.00260 (18456) covalent geometry : angle 0.54340 (25141) hydrogen bonds : bond 0.02802 ( 135) hydrogen bonds : angle 4.90270 ( 273) Misc. bond : bond 0.00170 ( 1) *********************** 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 236 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 0.786 Fit side-chains REVERT: A 40 THR cc_start: 0.8597 (m) cc_final: 0.8241 (p) REVERT: A 165 PHE cc_start: 0.8841 (m-10) cc_final: 0.8362 (m-10) REVERT: B 55 ASP cc_start: 0.8181 (t70) cc_final: 0.7455 (t0) REVERT: B 174 ASN cc_start: 0.8195 (t0) cc_final: 0.7662 (t0) REVERT: B 253 MET cc_start: 0.8578 (tpp) cc_final: 0.7976 (mmt) REVERT: D 15 MET cc_start: 0.8851 (mtm) cc_final: 0.8633 (mtm) REVERT: D 56 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8221 (mp) REVERT: D 101 GLU cc_start: 0.8764 (mp0) cc_final: 0.7475 (tm-30) REVERT: D 117 MET cc_start: 0.8935 (mpp) cc_final: 0.8669 (mtt) REVERT: E 89 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8531 (ttm) REVERT: E 134 ASP cc_start: 0.8240 (p0) cc_final: 0.7608 (t0) REVERT: E 148 MET cc_start: 0.9205 (tmm) cc_final: 0.8941 (tmm) REVERT: E 174 ASN cc_start: 0.8437 (t0) cc_final: 0.7905 (t0) REVERT: F 56 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8399 (mp) REVERT: F 117 MET cc_start: 0.8812 (mpp) cc_final: 0.8293 (mtt) REVERT: G 134 ASP cc_start: 0.8224 (p0) cc_final: 0.7573 (t0) REVERT: G 148 MET cc_start: 0.8998 (tmm) cc_final: 0.8745 (tmm) REVERT: G 174 ASN cc_start: 0.8422 (t0) cc_final: 0.7871 (t0) REVERT: G 245 GLU cc_start: 0.8368 (mp0) cc_final: 0.8034 (mp0) REVERT: H 40 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8716 (p) REVERT: H 69 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8778 (t) REVERT: H 70 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8894 (pt) REVERT: H 101 GLU cc_start: 0.8917 (mp0) cc_final: 0.7654 (tm-30) REVERT: H 112 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: H 147 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8553 (tt0) REVERT: H 163 MET cc_start: 0.9166 (mtt) cc_final: 0.8872 (mtt) REVERT: H 189 LEU cc_start: 0.7220 (tt) cc_final: 0.6787 (mp) REVERT: I 75 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.7818 (p) REVERT: I 89 MET cc_start: 0.9000 (ttp) cc_final: 0.8710 (ttp) REVERT: I 100 TYR cc_start: 0.8542 (p90) cc_final: 0.8268 (p90) REVERT: I 111 ASP cc_start: 0.6696 (m-30) cc_final: 0.6443 (m-30) REVERT: I 134 ASP cc_start: 0.8636 (p0) cc_final: 0.7799 (t70) REVERT: I 164 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8574 (t) REVERT: I 169 ASP cc_start: 0.8300 (m-30) cc_final: 0.7718 (p0) REVERT: I 174 ASN cc_start: 0.8634 (t0) cc_final: 0.8054 (t0) REVERT: I 245 GLU cc_start: 0.8360 (mp0) cc_final: 0.8043 (mp0) outliers start: 62 outliers final: 49 residues processed: 222 average time/residue: 0.1326 time to fit residues: 46.1437 Evaluate side-chains 222 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 164 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 215 LEU 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 357 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 125 ILE 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 89 MET Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain G residue 20 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 153 VAL Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 THR 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 112 GLN Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 333 SER Chi-restraints excluded: chain I residue 357 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 4 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 154 optimal weight: 0.0470 chunk 131 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 8 optimal weight: 0.3980 chunk 104 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- 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 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.093627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078324 restraints weight = 36808.634| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.31 r_work: 0.3024 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 1.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18457 Z= 0.096 Angle : 0.542 13.469 25141 Z= 0.254 Chirality : 0.043 0.153 2792 Planarity : 0.004 0.064 3245 Dihedral : 4.007 17.317 2459 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.27 % Allowed : 19.86 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.17), residues: 2289 helix: -1.56 (0.33), residues: 228 sheet: -0.08 (0.20), residues: 792 loop : -1.22 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 164 TYR 0.014 0.001 TYR D 145 PHE 0.011 0.001 PHE E 275 TRP 0.009 0.001 TRP I 156 HIS 0.003 0.001 HIS H 71 Details of bonding type rmsd covalent geometry : bond 0.00238 (18456) covalent geometry : angle 0.54192 (25141) hydrogen bonds : bond 0.02667 ( 135) hydrogen bonds : angle 4.79775 ( 273) Misc. bond : bond 0.00132 ( 1) *********************** 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 233 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 168 time to evaluate : 0.887 Fit side-chains REVERT: A 40 THR cc_start: 0.8593 (m) cc_final: 0.8244 (p) REVERT: A 165 PHE cc_start: 0.8797 (m-10) cc_final: 0.8251 (m-10) REVERT: B 55 ASP cc_start: 0.8166 (t70) cc_final: 0.7484 (t0) REVERT: B 174 ASN cc_start: 0.8235 (t0) cc_final: 0.7681 (t0) REVERT: B 249 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: B 253 MET cc_start: 0.8518 (tpp) cc_final: 0.7929 (mmt) REVERT: D 15 MET cc_start: 0.8854 (mtm) cc_final: 0.8598 (mtm) REVERT: D 56 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8302 (mp) REVERT: D 117 MET cc_start: 0.8889 (mpp) cc_final: 0.8672 (mtt) REVERT: E 89 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8505 (ttm) REVERT: E 134 ASP cc_start: 0.8280 (p0) cc_final: 0.7651 (t0) REVERT: E 148 MET cc_start: 0.9229 (tmm) cc_final: 0.8943 (tmm) REVERT: E 174 ASN cc_start: 0.8484 (t0) cc_final: 0.7952 (t0) REVERT: F 56 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8415 (mp) REVERT: F 101 GLU cc_start: 0.9182 (mp0) cc_final: 0.8882 (mp0) REVERT: F 117 MET cc_start: 0.8805 (mpp) cc_final: 0.8311 (mtt) REVERT: G 134 ASP cc_start: 0.8236 (p0) cc_final: 0.7566 (t0) REVERT: G 174 ASN cc_start: 0.8444 (t0) cc_final: 0.7897 (t0) REVERT: G 245 GLU cc_start: 0.8405 (mp0) cc_final: 0.8061 (mp0) REVERT: H 40 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8612 (p) REVERT: H 69 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8751 (t) REVERT: H 70 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8889 (pt) REVERT: H 101 GLU cc_start: 0.8935 (mp0) cc_final: 0.7642 (tm-30) REVERT: H 112 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: H 118 LEU cc_start: 0.8535 (mp) cc_final: 0.8148 (mt) REVERT: H 147 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8521 (tt0) REVERT: H 189 LEU cc_start: 0.7286 (tt) cc_final: 0.6868 (mp) REVERT: I 75 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.7830 (p) REVERT: I 89 MET cc_start: 0.9012 (ttp) cc_final: 0.8729 (ttp) REVERT: I 111 ASP cc_start: 0.6681 (m-30) cc_final: 0.6418 (m-30) REVERT: I 134 ASP cc_start: 0.8679 (p0) cc_final: 0.7846 (t70) REVERT: I 164 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8700 (t) REVERT: I 169 ASP cc_start: 0.8285 (m-30) cc_final: 0.7725 (p0) REVERT: I 174 ASN cc_start: 0.8640 (t0) cc_final: 0.8077 (t0) REVERT: I 245 GLU cc_start: 0.8269 (mp0) cc_final: 0.7971 (mp0) REVERT: I 332 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8449 (p0) outliers start: 65 outliers final: 43 residues processed: 219 average time/residue: 0.1352 time to fit residues: 47.2328 Evaluate side-chains 219 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 249 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 357 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 125 ILE 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 89 MET Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain G residue 20 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 153 VAL Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 THR 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 112 GLN Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain I residue 333 SER Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 363 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 176 optimal weight: 2.9990 chunk 214 optimal weight: 0.0770 chunk 141 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- 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 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.090248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.075151 restraints weight = 37021.260| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.24 r_work: 0.2963 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 1.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18457 Z= 0.184 Angle : 0.608 14.982 25141 Z= 0.290 Chirality : 0.045 0.152 2792 Planarity : 0.004 0.063 3245 Dihedral : 4.346 18.558 2459 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.92 % Allowed : 20.36 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.17), residues: 2289 helix: -1.75 (0.32), residues: 228 sheet: -0.23 (0.20), residues: 804 loop : -1.36 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 164 TYR 0.015 0.002 TYR A 93 PHE 0.017 0.002 PHE A 165 TRP 0.013 0.001 TRP A 144 HIS 0.003 0.001 HIS E 283 Details of bonding type rmsd covalent geometry : bond 0.00453 (18456) covalent geometry : angle 0.60821 (25141) hydrogen bonds : bond 0.03545 ( 135) hydrogen bonds : angle 5.04443 ( 273) Misc. bond : bond 0.00059 ( 1) ********************** 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 219 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 0.727 Fit side-chains REVERT: A 40 THR cc_start: 0.8641 (m) cc_final: 0.8255 (p) REVERT: A 69 THR cc_start: 0.8869 (m) cc_final: 0.8558 (p) REVERT: A 101 GLU cc_start: 0.9110 (mp0) cc_final: 0.8731 (mp0) REVERT: B 36 MET cc_start: 0.8635 (ptt) cc_final: 0.8355 (ptt) REVERT: B 55 ASP cc_start: 0.8282 (t70) cc_final: 0.7626 (t0) REVERT: B 174 ASN cc_start: 0.8527 (t0) cc_final: 0.8046 (t0) REVERT: B 178 GLU cc_start: 0.7130 (pp20) cc_final: 0.6887 (pm20) REVERT: B 249 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: D 56 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8541 (mp) REVERT: D 117 MET cc_start: 0.9060 (mpp) cc_final: 0.8772 (mtt) REVERT: E 134 ASP cc_start: 0.8265 (p0) cc_final: 0.7623 (t0) REVERT: E 151 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9199 (pt) REVERT: E 174 ASN cc_start: 0.8621 (t0) cc_final: 0.8101 (t0) REVERT: F 56 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8550 (mp) REVERT: F 117 MET cc_start: 0.9017 (mpp) cc_final: 0.8485 (mtt) REVERT: G 174 ASN cc_start: 0.8581 (t0) cc_final: 0.8066 (t0) REVERT: G 245 GLU cc_start: 0.8413 (mp0) cc_final: 0.8055 (mp0) REVERT: H 40 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8730 (p) REVERT: H 70 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8939 (pt) REVERT: H 101 GLU cc_start: 0.8911 (mp0) cc_final: 0.7684 (tm-30) REVERT: H 112 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: H 147 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8574 (tt0) REVERT: H 189 LEU cc_start: 0.7366 (tt) cc_final: 0.6930 (mp) REVERT: I 75 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.7775 (p) REVERT: I 89 MET cc_start: 0.9047 (ttp) cc_final: 0.8782 (ttp) REVERT: I 96 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8864 (p) REVERT: I 111 ASP cc_start: 0.6869 (m-30) cc_final: 0.6618 (m-30) REVERT: I 134 ASP cc_start: 0.8625 (p0) cc_final: 0.7841 (t0) REVERT: I 164 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8820 (t) REVERT: I 169 ASP cc_start: 0.8259 (m-30) cc_final: 0.7728 (p0) REVERT: I 174 ASN cc_start: 0.8714 (t0) cc_final: 0.8103 (t0) REVERT: I 245 GLU cc_start: 0.8246 (mp0) cc_final: 0.7975 (mp0) REVERT: I 332 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8530 (p0) outliers start: 58 outliers final: 39 residues processed: 210 average time/residue: 0.1314 time to fit residues: 44.2560 Evaluate side-chains 208 residues out of total 1989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 249 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 357 ILE Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 125 ILE 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 151 ILE Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain G residue 20 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 153 VAL Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain I residue 333 SER Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 363 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 127 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.092057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.076662 restraints weight = 36983.187| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.34 r_work: 0.2994 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 1.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18457 Z= 0.107 Angle : 0.552 13.381 25141 Z= 0.259 Chirality : 0.043 0.154 2792 Planarity : 0.004 0.065 3245 Dihedral : 4.160 17.298 2459 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.82 % Allowed : 20.21 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.17), residues: 2289 helix: -1.72 (0.32), residues: 232 sheet: -0.17 (0.20), residues: 810 loop : -1.24 (0.16), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 211 TYR 0.010 0.001 TYR B 182 PHE 0.013 0.001 PHE A 165 TRP 0.011 0.001 TRP A 144 HIS 0.002 0.001 HIS H 71 Details of bonding type rmsd covalent geometry : bond 0.00267 (18456) covalent geometry : angle 0.55233 (25141) hydrogen bonds : bond 0.02859 ( 135) hydrogen bonds : angle 4.79830 ( 273) Misc. bond : bond 0.00113 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4633.51 seconds wall clock time: 80 minutes 3.83 seconds (4803.83 seconds total)