Starting phenix.real_space_refine on Sun Mar 10 21:33:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/03_2024/7nnh_12477.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/03_2024/7nnh_12477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/03_2024/7nnh_12477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/03_2024/7nnh_12477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/03_2024/7nnh_12477.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/03_2024/7nnh_12477.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 3332 2.51 5 N 916 2.21 5 O 1013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X ASP 1996": "OD1" <-> "OD2" Residue "X ASP 2008": "OD1" <-> "OD2" Residue "X ASP 2014": "OD1" <-> "OD2" Residue "X ASP 2019": "OD1" <-> "OD2" Residue "X PHE 2050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 2069": "OE1" <-> "OE2" Residue "X PHE 2080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 2087": "OE1" <-> "OE2" Residue "X GLU 2092": "OE1" <-> "OE2" Residue "X TYR 2103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 2106": "OE1" <-> "OE2" Residue "X ASP 2122": "OD1" <-> "OD2" Residue "X GLU 2132": "OE1" <-> "OE2" Residue "X ASP 2143": "OD1" <-> "OD2" Residue "X ASP 2169": "OD1" <-> "OD2" Residue "X GLU 2222": "OE1" <-> "OE2" Residue "X TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 2258": "OD1" <-> "OD2" Residue "X ASP 2294": "OD1" <-> "OD2" Residue "X GLU 2296": "OE1" <-> "OE2" Residue "X GLU 2298": "OE1" <-> "OE2" Residue "X PHE 2300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 2326": "OD1" <-> "OD2" Residue "X GLU 2405": "OE1" <-> "OE2" Residue "X TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 2428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 2430": "OD1" <-> "OD2" Residue "X ASP 2439": "OD1" <-> "OD2" Residue "X GLU 2490": "OE1" <-> "OE2" Residue "X ASP 2499": "OD1" <-> "OD2" Residue "X GLU 2512": "OE1" <-> "OE2" Residue "X GLU 2536": "OE1" <-> "OE2" Residue "X GLU 2600": "OE1" <-> "OE2" Residue "X GLU 2621": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5299 Number of models: 1 Model: "" Number of chains: 1 Chain: "X" Number of atoms: 5299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5299 Classifications: {'peptide': 637} Link IDs: {'CIS': 19, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 598} Time building chain proxies: 3.30, per 1000 atoms: 0.62 Number of scatterers: 5299 At special positions: 0 Unit cell: (74.7, 123.67, 98.77, 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 38 16.00 O 1013 8.00 N 916 7.00 C 3332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS X1993 " - pdb=" SG CYS X2173 " distance=2.03 Simple disulfide: pdb=" SG CYS X2003 " - pdb=" SG CYS X2158 " distance=2.02 Simple disulfide: pdb=" SG CYS X2012 " - pdb=" SG CYS X2049 " distance=2.03 Simple disulfide: pdb=" SG CYS X2210 " - pdb=" SG CYS X2226 " distance=2.03 Simple disulfide: pdb=" SG CYS X2276 " - pdb=" SG CYS X2279 " distance=2.04 Simple disulfide: pdb=" SG CYS X2333 " - pdb=" SG CYS X2480 " distance=2.03 Simple disulfide: pdb=" SG CYS X2518 " - pdb=" SG CYS X2601 " distance=2.03 Simple disulfide: pdb=" SG CYS X2532 " - pdb=" SG CYS X2547 " distance=2.03 Simple disulfide: pdb=" SG CYS X2594 " - pdb=" SG CYS X2599 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 906.6 milliseconds 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1222 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 48.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'X' and resid 2000 through 2006 removed outlier: 4.081A pdb=" N ASP X2004 " --> pdb=" O MET X2000 " (cutoff:3.500A) Processing helix chain 'X' and resid 2083 through 2089 removed outlier: 4.261A pdb=" N GLU X2087 " --> pdb=" O ASN X2083 " (cutoff:3.500A) Processing helix chain 'X' and resid 2090 through 2111 removed outlier: 4.076A pdb=" N ALA X2094 " --> pdb=" O ASP X2090 " (cutoff:3.500A) Processing helix chain 'X' and resid 2122 through 2133 Processing helix chain 'X' and resid 2139 through 2145 Processing helix chain 'X' and resid 2169 through 2174 Processing helix chain 'X' and resid 2182 through 2209 removed outlier: 4.328A pdb=" N GLN X2198 " --> pdb=" O ASN X2194 " (cutoff:3.500A) Processing helix chain 'X' and resid 2224 through 2250 removed outlier: 4.023A pdb=" N SER X2228 " --> pdb=" O ASN X2224 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE X2230 " --> pdb=" O CYS X2226 " (cutoff:3.500A) Processing helix chain 'X' and resid 2267 through 2275 Processing helix chain 'X' and resid 2308 through 2315 removed outlier: 4.494A pdb=" N ASP X2315 " --> pdb=" O ALA X2311 " (cutoff:3.500A) Processing helix chain 'X' and resid 2331 through 2340 Processing helix chain 'X' and resid 2354 through 2358 removed outlier: 3.645A pdb=" N LYS X2357 " --> pdb=" O ASN X2354 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS X2358 " --> pdb=" O PHE X2355 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 2354 through 2358' Processing helix chain 'X' and resid 2369 through 2374 removed outlier: 4.336A pdb=" N ASN X2374 " --> pdb=" O PRO X2370 " (cutoff:3.500A) Processing helix chain 'X' and resid 2390 through 2414 Processing helix chain 'X' and resid 2416 through 2437 removed outlier: 3.646A pdb=" N HIS X2422 " --> pdb=" O ALA X2418 " (cutoff:3.500A) Processing helix chain 'X' and resid 2444 through 2452 Processing helix chain 'X' and resid 2460 through 2487 removed outlier: 3.611A pdb=" N ASP X2468 " --> pdb=" O LYS X2464 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET X2469 " --> pdb=" O LYS X2465 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N TYR X2472 " --> pdb=" O ASP X2468 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N HIS X2473 " --> pdb=" O MET X2469 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU X2484 " --> pdb=" O CYS X2480 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA X2485 " --> pdb=" O GLY X2481 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU X2486 " --> pdb=" O TYR X2482 " (cutoff:3.500A) Processing helix chain 'X' and resid 2498 through 2502 Processing helix chain 'X' and resid 2504 through 2516 Processing helix chain 'X' and resid 2519 through 2528 Processing helix chain 'X' and resid 2544 through 2576 Processing helix chain 'X' and resid 2585 through 2594 205 hydrogen bonds defined for protein. 609 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: 1.24 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1720 1.34 - 1.47: 1260 1.47 - 1.60: 2382 1.60 - 1.72: 0 1.72 - 1.85: 52 Bond restraints: 5414 Sorted by residual: bond pdb=" C HIS X2322 " pdb=" O HIS X2322 " ideal model delta sigma weight residual 1.235 1.216 0.019 1.26e-02 6.30e+03 2.38e+00 bond pdb=" N GLU X2305 " pdb=" CA GLU X2305 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.20e+00 bond pdb=" C TYR X2251 " pdb=" N LYS X2252 " ideal model delta sigma weight residual 1.329 1.348 -0.019 1.40e-02 5.10e+03 1.84e+00 bond pdb=" CA PHE X2300 " pdb=" C PHE X2300 " ideal model delta sigma weight residual 1.524 1.543 -0.019 1.43e-02 4.89e+03 1.76e+00 bond pdb=" C LYS X2297 " pdb=" N GLU X2298 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.40e-02 5.10e+03 1.74e+00 ... (remaining 5409 not shown) Histogram of bond angle deviations from ideal: 99.33 - 107.61: 200 107.61 - 115.89: 3208 115.89 - 124.17: 3679 124.17 - 132.45: 162 132.45 - 140.73: 20 Bond angle restraints: 7269 Sorted by residual: angle pdb=" N ASN X2291 " pdb=" CA ASN X2291 " pdb=" C ASN X2291 " ideal model delta sigma weight residual 110.91 120.42 -9.51 1.17e+00 7.31e-01 6.61e+01 angle pdb=" N ASP X2285 " pdb=" CA ASP X2285 " pdb=" C ASP X2285 " ideal model delta sigma weight residual 113.31 99.33 13.98 2.04e+00 2.40e-01 4.69e+01 angle pdb=" N ASP X2519 " pdb=" CA ASP X2519 " pdb=" C ASP X2519 " ideal model delta sigma weight residual 113.88 106.08 7.80 1.23e+00 6.61e-01 4.02e+01 angle pdb=" C GLU X2324 " pdb=" N TYR X2325 " pdb=" CA TYR X2325 " ideal model delta sigma weight residual 121.70 132.88 -11.18 1.80e+00 3.09e-01 3.86e+01 angle pdb=" C CYS X2279 " pdb=" N PRO X2280 " pdb=" CD PRO X2280 " ideal model delta sigma weight residual 120.60 107.22 13.38 2.20e+00 2.07e-01 3.70e+01 ... (remaining 7264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.32: 3176 26.32 - 52.64: 152 52.64 - 78.96: 20 78.96 - 105.28: 2 105.28 - 131.60: 4 Dihedral angle restraints: 3354 sinusoidal: 1466 harmonic: 1888 Sorted by residual: dihedral pdb=" CA ASN X2290 " pdb=" C ASN X2290 " pdb=" N ASN X2291 " pdb=" CA ASN X2291 " ideal model delta harmonic sigma weight residual -180.00 -48.40 -131.60 0 5.00e+00 4.00e-02 6.93e+02 dihedral pdb=" CA LYS X2304 " pdb=" C LYS X2304 " pdb=" N GLU X2305 " pdb=" CA GLU X2305 " ideal model delta harmonic sigma weight residual 180.00 50.07 129.93 0 5.00e+00 4.00e-02 6.75e+02 dihedral pdb=" CA LYS X2321 " pdb=" C LYS X2321 " pdb=" N HIS X2322 " pdb=" CA HIS X2322 " ideal model delta harmonic sigma weight residual 180.00 61.27 118.73 0 5.00e+00 4.00e-02 5.64e+02 ... (remaining 3351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 585 0.058 - 0.117: 127 0.117 - 0.175: 17 0.175 - 0.234: 7 0.234 - 0.292: 2 Chirality restraints: 738 Sorted by residual: chirality pdb=" CA TYR X2325 " pdb=" N TYR X2325 " pdb=" C TYR X2325 " pdb=" CB TYR X2325 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ASP X2326 " pdb=" N ASP X2326 " pdb=" C ASP X2326 " pdb=" CB ASP X2326 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA GLU X2305 " pdb=" N GLU X2305 " pdb=" C GLU X2305 " pdb=" CB GLU X2305 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 735 not shown) Planarity restraints: 938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP X2145 " -0.021 2.00e-02 2.50e+03 1.78e-02 7.89e+00 pdb=" CG TRP X2145 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP X2145 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP X2145 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP X2145 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP X2145 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP X2145 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP X2145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP X2145 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP X2145 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X2244 " 0.023 2.00e-02 2.50e+03 1.71e-02 7.34e+00 pdb=" CG TRP X2244 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP X2244 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP X2244 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP X2244 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP X2244 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP X2244 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP X2244 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP X2244 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP X2244 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP X2380 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO X2381 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO X2381 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO X2381 " 0.031 5.00e-02 4.00e+02 ... (remaining 935 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 153 2.63 - 3.20: 5907 3.20 - 3.77: 9243 3.77 - 4.33: 12464 4.33 - 4.90: 18196 Nonbonded interactions: 45963 Sorted by model distance: nonbonded pdb=" O PHE X1994 " pdb=" OG1 THR X1998 " model vdw 2.066 2.440 nonbonded pdb=" O GLU X2245 " pdb=" OG SER X2248 " model vdw 2.112 2.440 nonbonded pdb=" OD1 ASN X2290 " pdb=" ND2 ASN X2292 " model vdw 2.163 2.520 nonbonded pdb=" O SER X2076 " pdb=" OH TYR X2085 " model vdw 2.175 2.440 nonbonded pdb=" O ASN X2374 " pdb=" NH1 ARG X2408 " model vdw 2.176 2.520 ... (remaining 45958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.260 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.320 Find NCS groups from input model: 0.130 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.004 0.055 5414 Z= 0.265 Angle : 1.283 13.978 7269 Z= 0.753 Chirality : 0.052 0.292 738 Planarity : 0.006 0.056 938 Dihedral : 15.824 131.595 2105 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 35.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 22.99 % Favored : 76.54 % Rotamer: Outliers : 0.34 % Allowed : 1.19 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 0.00 % Twisted General : 1.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.29), residues: 635 helix: -0.57 (0.28), residues: 274 sheet: None (None), residues: 0 loop : -4.17 (0.25), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP X2145 HIS 0.006 0.001 HIS X2322 PHE 0.030 0.002 PHE X2300 TYR 0.034 0.002 TYR X2325 ARG 0.007 0.001 ARG X2052 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2245 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8938 (mm-30) REVERT: X 2511 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8897 (tm-30) REVERT: X 2517 PHE cc_start: 0.8774 (t80) cc_final: 0.8249 (t80) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.2335 time to fit residues: 19.4586 Evaluate side-chains 44 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.0170 chunk 57 optimal weight: 0.9980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X2083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5414 Z= 0.219 Angle : 1.038 15.588 7269 Z= 0.544 Chirality : 0.050 0.266 738 Planarity : 0.006 0.052 938 Dihedral : 9.351 58.149 693 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 28.57 Ramachandran Plot: Outliers : 0.79 % Allowed : 20.16 % Favored : 79.06 % Rotamer: Outliers : 1.19 % Allowed : 11.71 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 1.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.30), residues: 635 helix: 0.11 (0.30), residues: 269 sheet: None (None), residues: 0 loop : -3.93 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP X2244 HIS 0.008 0.001 HIS X2322 PHE 0.020 0.002 PHE X2066 TYR 0.031 0.002 TYR X2325 ARG 0.005 0.001 ARG X2372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2114 MET cc_start: 0.9020 (mpp) cc_final: 0.8548 (pmm) REVERT: X 2245 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8954 (mm-30) REVERT: X 2286 MET cc_start: 0.8908 (mmm) cc_final: 0.8682 (mmm) REVERT: X 2424 MET cc_start: 0.9480 (mtm) cc_final: 0.9201 (mtp) REVERT: X 2438 ASP cc_start: 0.8910 (m-30) cc_final: 0.8355 (p0) REVERT: X 2511 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8864 (tm-30) REVERT: X 2517 PHE cc_start: 0.8629 (t80) cc_final: 0.8154 (t80) REVERT: X 2555 LYS cc_start: 0.9698 (pptt) cc_final: 0.9492 (pptt) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.2561 time to fit residues: 18.2532 Evaluate side-chains 48 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 2002 VAL Chi-restraints excluded: chain X residue 2140 LYS Chi-restraints excluded: chain X residue 2230 ILE Chi-restraints excluded: chain X residue 2377 LEU Chi-restraints excluded: chain X residue 2554 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X2047 GLN X2083 ASN ** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X2556 ASN ** X2570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X2574 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5414 Z= 0.213 Angle : 0.970 12.641 7269 Z= 0.512 Chirality : 0.048 0.237 738 Planarity : 0.005 0.052 938 Dihedral : 8.629 42.849 693 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 30.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 20.63 % Favored : 79.21 % Rotamer: Outliers : 2.55 % Allowed : 15.28 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 0.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.31), residues: 635 helix: 0.17 (0.30), residues: 272 sheet: None (None), residues: 0 loop : -3.85 (0.27), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP X2144 HIS 0.003 0.001 HIS X2036 PHE 0.018 0.002 PHE X2066 TYR 0.023 0.002 TYR X2325 ARG 0.009 0.001 ARG X2129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2114 MET cc_start: 0.8983 (mpp) cc_final: 0.8550 (pmm) REVERT: X 2139 LYS cc_start: 0.9796 (pttm) cc_final: 0.9586 (ptmt) REVERT: X 2245 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8957 (mm-30) REVERT: X 2424 MET cc_start: 0.9519 (mtm) cc_final: 0.9108 (mtp) REVERT: X 2461 GLU cc_start: 0.9452 (tm-30) cc_final: 0.8828 (tm-30) REVERT: X 2511 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8875 (tm-30) REVERT: X 2517 PHE cc_start: 0.8637 (t80) cc_final: 0.8147 (t80) REVERT: X 2555 LYS cc_start: 0.9707 (pptt) cc_final: 0.9485 (pptt) outliers start: 15 outliers final: 11 residues processed: 63 average time/residue: 0.2192 time to fit residues: 17.6343 Evaluate side-chains 53 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 2002 VAL Chi-restraints excluded: chain X residue 2016 THR Chi-restraints excluded: chain X residue 2066 PHE Chi-restraints excluded: chain X residue 2140 LYS Chi-restraints excluded: chain X residue 2226 CYS Chi-restraints excluded: chain X residue 2263 VAL Chi-restraints excluded: chain X residue 2377 LEU Chi-restraints excluded: chain X residue 2407 GLU Chi-restraints excluded: chain X residue 2426 TYR Chi-restraints excluded: chain X residue 2554 TYR Chi-restraints excluded: chain X residue 2568 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X2047 GLN X2083 ASN ** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5414 Z= 0.198 Angle : 0.963 17.287 7269 Z= 0.499 Chirality : 0.047 0.231 738 Planarity : 0.005 0.052 938 Dihedral : 8.276 42.362 693 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 28.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 20.31 % Favored : 79.37 % Rotamer: Outliers : 3.40 % Allowed : 16.47 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 0.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.31), residues: 635 helix: 0.17 (0.30), residues: 273 sheet: None (None), residues: 0 loop : -3.86 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP X2144 HIS 0.004 0.001 HIS X2322 PHE 0.015 0.001 PHE X2066 TYR 0.020 0.002 TYR X2325 ARG 0.007 0.001 ARG X2129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2027 MET cc_start: 0.8836 (mmp) cc_final: 0.8069 (ptp) REVERT: X 2114 MET cc_start: 0.8973 (mpp) cc_final: 0.8567 (pmm) REVERT: X 2139 LYS cc_start: 0.9801 (pttm) cc_final: 0.9592 (ptmt) REVERT: X 2245 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8992 (mm-30) REVERT: X 2247 ILE cc_start: 0.8451 (mm) cc_final: 0.8181 (mm) REVERT: X 2289 MET cc_start: 0.6601 (mmm) cc_final: 0.6396 (mmm) REVERT: X 2424 MET cc_start: 0.9506 (mtm) cc_final: 0.9269 (mtp) REVERT: X 2478 MET cc_start: 0.9572 (mtp) cc_final: 0.8926 (ttm) REVERT: X 2511 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8858 (tm-30) REVERT: X 2517 PHE cc_start: 0.8668 (t80) cc_final: 0.8208 (t80) REVERT: X 2555 LYS cc_start: 0.9729 (pptt) cc_final: 0.9495 (pptt) outliers start: 20 outliers final: 14 residues processed: 62 average time/residue: 0.2140 time to fit residues: 16.9876 Evaluate side-chains 58 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 2002 VAL Chi-restraints excluded: chain X residue 2016 THR Chi-restraints excluded: chain X residue 2066 PHE Chi-restraints excluded: chain X residue 2083 ASN Chi-restraints excluded: chain X residue 2140 LYS Chi-restraints excluded: chain X residue 2226 CYS Chi-restraints excluded: chain X residue 2263 VAL Chi-restraints excluded: chain X residue 2285 ASP Chi-restraints excluded: chain X residue 2377 LEU Chi-restraints excluded: chain X residue 2407 GLU Chi-restraints excluded: chain X residue 2426 TYR Chi-restraints excluded: chain X residue 2547 CYS Chi-restraints excluded: chain X residue 2554 TYR Chi-restraints excluded: chain X residue 2568 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2083 ASN ** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5414 Z= 0.257 Angle : 0.967 17.105 7269 Z= 0.510 Chirality : 0.047 0.238 738 Planarity : 0.005 0.049 938 Dihedral : 8.337 41.908 693 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 34.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 21.10 % Favored : 78.58 % Rotamer: Outliers : 3.23 % Allowed : 18.34 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 0.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.31), residues: 635 helix: 0.35 (0.31), residues: 261 sheet: None (None), residues: 0 loop : -3.76 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP X2144 HIS 0.003 0.001 HIS X2036 PHE 0.016 0.002 PHE X2066 TYR 0.024 0.002 TYR X2325 ARG 0.006 0.001 ARG X2372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2114 MET cc_start: 0.8955 (mpp) cc_final: 0.8609 (pmm) REVERT: X 2139 LYS cc_start: 0.9796 (pttm) cc_final: 0.9590 (ptmt) REVERT: X 2245 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8980 (mm-30) REVERT: X 2247 ILE cc_start: 0.8564 (mm) cc_final: 0.8284 (mm) REVERT: X 2424 MET cc_start: 0.9527 (mtm) cc_final: 0.9171 (mtp) REVERT: X 2511 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8921 (tm-30) REVERT: X 2517 PHE cc_start: 0.8692 (t80) cc_final: 0.8255 (t80) REVERT: X 2555 LYS cc_start: 0.9746 (pptt) cc_final: 0.9515 (pptt) outliers start: 19 outliers final: 16 residues processed: 59 average time/residue: 0.2179 time to fit residues: 16.2426 Evaluate side-chains 58 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 2016 THR Chi-restraints excluded: chain X residue 2066 PHE Chi-restraints excluded: chain X residue 2084 TYR Chi-restraints excluded: chain X residue 2140 LYS Chi-restraints excluded: chain X residue 2205 TYR Chi-restraints excluded: chain X residue 2226 CYS Chi-restraints excluded: chain X residue 2236 TRP Chi-restraints excluded: chain X residue 2263 VAL Chi-restraints excluded: chain X residue 2285 ASP Chi-restraints excluded: chain X residue 2377 LEU Chi-restraints excluded: chain X residue 2407 GLU Chi-restraints excluded: chain X residue 2426 TYR Chi-restraints excluded: chain X residue 2440 MET Chi-restraints excluded: chain X residue 2547 CYS Chi-restraints excluded: chain X residue 2554 TYR Chi-restraints excluded: chain X residue 2568 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.0060 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2136 ASN ** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5414 Z= 0.192 Angle : 0.931 14.369 7269 Z= 0.486 Chirality : 0.046 0.232 738 Planarity : 0.005 0.051 938 Dihedral : 8.122 42.033 693 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 28.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 20.63 % Favored : 79.06 % Rotamer: Outliers : 3.06 % Allowed : 19.69 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.31), residues: 635 helix: 0.41 (0.30), residues: 261 sheet: None (None), residues: 0 loop : -3.70 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP X2144 HIS 0.004 0.001 HIS X2322 PHE 0.016 0.001 PHE X2066 TYR 0.019 0.001 TYR X2325 ARG 0.004 0.000 ARG X2372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2027 MET cc_start: 0.8846 (mmp) cc_final: 0.8055 (ptp) REVERT: X 2114 MET cc_start: 0.8936 (mpp) cc_final: 0.8610 (pmm) REVERT: X 2199 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8869 (mtpt) REVERT: X 2245 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8945 (mm-30) REVERT: X 2247 ILE cc_start: 0.8416 (mm) cc_final: 0.8132 (mm) REVERT: X 2289 MET cc_start: 0.6855 (mmm) cc_final: 0.6637 (mmt) REVERT: X 2424 MET cc_start: 0.9503 (mtm) cc_final: 0.9086 (mtp) REVERT: X 2511 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8865 (tm-30) REVERT: X 2517 PHE cc_start: 0.8690 (t80) cc_final: 0.8225 (t80) REVERT: X 2555 LYS cc_start: 0.9735 (pptt) cc_final: 0.9492 (pptt) outliers start: 18 outliers final: 16 residues processed: 61 average time/residue: 0.2382 time to fit residues: 18.2519 Evaluate side-chains 60 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 2016 THR Chi-restraints excluded: chain X residue 2041 ILE Chi-restraints excluded: chain X residue 2066 PHE Chi-restraints excluded: chain X residue 2140 LYS Chi-restraints excluded: chain X residue 2178 THR Chi-restraints excluded: chain X residue 2226 CYS Chi-restraints excluded: chain X residue 2236 TRP Chi-restraints excluded: chain X residue 2263 VAL Chi-restraints excluded: chain X residue 2285 ASP Chi-restraints excluded: chain X residue 2377 LEU Chi-restraints excluded: chain X residue 2407 GLU Chi-restraints excluded: chain X residue 2426 TYR Chi-restraints excluded: chain X residue 2440 MET Chi-restraints excluded: chain X residue 2547 CYS Chi-restraints excluded: chain X residue 2554 TYR Chi-restraints excluded: chain X residue 2568 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2284 ASN ** X2582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5414 Z= 0.190 Angle : 0.919 14.706 7269 Z= 0.481 Chirality : 0.046 0.239 738 Planarity : 0.005 0.050 938 Dihedral : 7.921 41.064 693 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 30.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 21.73 % Favored : 78.11 % Rotamer: Outliers : 3.23 % Allowed : 20.37 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.31), residues: 635 helix: 0.50 (0.30), residues: 263 sheet: None (None), residues: 0 loop : -3.75 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP X2144 HIS 0.003 0.001 HIS X2322 PHE 0.017 0.001 PHE X2066 TYR 0.022 0.001 TYR X2325 ARG 0.004 0.000 ARG X2129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2065 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8495 (mp0) REVERT: X 2114 MET cc_start: 0.8943 (mpp) cc_final: 0.8616 (pmm) REVERT: X 2245 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8974 (mm-30) REVERT: X 2289 MET cc_start: 0.7176 (mmm) cc_final: 0.6966 (mmt) REVERT: X 2424 MET cc_start: 0.9500 (mtm) cc_final: 0.9073 (mtp) REVERT: X 2511 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8869 (tm-30) REVERT: X 2517 PHE cc_start: 0.8692 (t80) cc_final: 0.8080 (t80) REVERT: X 2526 ASP cc_start: 0.9391 (m-30) cc_final: 0.9168 (p0) REVERT: X 2555 LYS cc_start: 0.9743 (pptt) cc_final: 0.9507 (pptt) REVERT: X 2601 CYS cc_start: 0.6004 (OUTLIER) cc_final: 0.5423 (p) outliers start: 19 outliers final: 17 residues processed: 62 average time/residue: 0.2272 time to fit residues: 17.9334 Evaluate side-chains 63 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 2012 CYS Chi-restraints excluded: chain X residue 2016 THR Chi-restraints excluded: chain X residue 2041 ILE Chi-restraints excluded: chain X residue 2066 PHE Chi-restraints excluded: chain X residue 2140 LYS Chi-restraints excluded: chain X residue 2178 THR Chi-restraints excluded: chain X residue 2226 CYS Chi-restraints excluded: chain X residue 2236 TRP Chi-restraints excluded: chain X residue 2263 VAL Chi-restraints excluded: chain X residue 2285 ASP Chi-restraints excluded: chain X residue 2377 LEU Chi-restraints excluded: chain X residue 2407 GLU Chi-restraints excluded: chain X residue 2426 TYR Chi-restraints excluded: chain X residue 2440 MET Chi-restraints excluded: chain X residue 2547 CYS Chi-restraints excluded: chain X residue 2554 TYR Chi-restraints excluded: chain X residue 2568 GLN Chi-restraints excluded: chain X residue 2601 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5414 Z= 0.200 Angle : 0.934 15.381 7269 Z= 0.484 Chirality : 0.046 0.237 738 Planarity : 0.005 0.050 938 Dihedral : 7.889 40.622 693 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 21.42 % Favored : 78.43 % Rotamer: Outliers : 3.74 % Allowed : 20.71 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.31), residues: 635 helix: 0.52 (0.30), residues: 263 sheet: None (None), residues: 0 loop : -3.74 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X2144 HIS 0.004 0.001 HIS X2322 PHE 0.016 0.001 PHE X2066 TYR 0.022 0.001 TYR X2325 ARG 0.003 0.001 ARG X2129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2114 MET cc_start: 0.8938 (mpp) cc_final: 0.8626 (pmm) REVERT: X 2245 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8980 (mm-30) REVERT: X 2289 MET cc_start: 0.7221 (mmm) cc_final: 0.6988 (mmt) REVERT: X 2424 MET cc_start: 0.9501 (mtm) cc_final: 0.9073 (mtp) REVERT: X 2511 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8878 (tm-30) REVERT: X 2517 PHE cc_start: 0.8709 (t80) cc_final: 0.8088 (t80) REVERT: X 2526 ASP cc_start: 0.9385 (m-30) cc_final: 0.9153 (p0) REVERT: X 2555 LYS cc_start: 0.9747 (pptt) cc_final: 0.9508 (pptt) REVERT: X 2601 CYS cc_start: 0.5886 (OUTLIER) cc_final: 0.5263 (p) outliers start: 22 outliers final: 18 residues processed: 64 average time/residue: 0.2155 time to fit residues: 17.6764 Evaluate side-chains 64 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 2012 CYS Chi-restraints excluded: chain X residue 2016 THR Chi-restraints excluded: chain X residue 2041 ILE Chi-restraints excluded: chain X residue 2066 PHE Chi-restraints excluded: chain X residue 2140 LYS Chi-restraints excluded: chain X residue 2178 THR Chi-restraints excluded: chain X residue 2226 CYS Chi-restraints excluded: chain X residue 2234 GLN Chi-restraints excluded: chain X residue 2236 TRP Chi-restraints excluded: chain X residue 2263 VAL Chi-restraints excluded: chain X residue 2285 ASP Chi-restraints excluded: chain X residue 2377 LEU Chi-restraints excluded: chain X residue 2407 GLU Chi-restraints excluded: chain X residue 2426 TYR Chi-restraints excluded: chain X residue 2440 MET Chi-restraints excluded: chain X residue 2547 CYS Chi-restraints excluded: chain X residue 2554 TYR Chi-restraints excluded: chain X residue 2568 GLN Chi-restraints excluded: chain X residue 2601 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 0.0020 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5414 Z= 0.197 Angle : 0.935 14.523 7269 Z= 0.482 Chirality : 0.046 0.252 738 Planarity : 0.005 0.050 938 Dihedral : 7.852 40.855 693 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 30.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 21.26 % Favored : 78.43 % Rotamer: Outliers : 3.40 % Allowed : 21.39 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.31), residues: 635 helix: 0.59 (0.30), residues: 263 sheet: None (None), residues: 0 loop : -3.72 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X2144 HIS 0.005 0.001 HIS X2322 PHE 0.017 0.001 PHE X2066 TYR 0.024 0.001 TYR X2325 ARG 0.004 0.000 ARG X2129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2065 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8379 (mp0) REVERT: X 2114 MET cc_start: 0.8913 (mpp) cc_final: 0.8645 (pmm) REVERT: X 2245 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8996 (mm-30) REVERT: X 2289 MET cc_start: 0.7286 (mmm) cc_final: 0.7075 (mmt) REVERT: X 2424 MET cc_start: 0.9492 (mtm) cc_final: 0.9068 (mtp) REVERT: X 2511 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8877 (tm-30) REVERT: X 2517 PHE cc_start: 0.8728 (t80) cc_final: 0.8033 (t80) REVERT: X 2521 ARG cc_start: 0.9160 (mtm110) cc_final: 0.8726 (mtm110) REVERT: X 2526 ASP cc_start: 0.9388 (m-30) cc_final: 0.9146 (p0) REVERT: X 2555 LYS cc_start: 0.9748 (pptt) cc_final: 0.9510 (pptt) REVERT: X 2601 CYS cc_start: 0.5984 (OUTLIER) cc_final: 0.5236 (p) outliers start: 20 outliers final: 19 residues processed: 63 average time/residue: 0.2619 time to fit residues: 21.3513 Evaluate side-chains 66 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 2012 CYS Chi-restraints excluded: chain X residue 2016 THR Chi-restraints excluded: chain X residue 2041 ILE Chi-restraints excluded: chain X residue 2066 PHE Chi-restraints excluded: chain X residue 2140 LYS Chi-restraints excluded: chain X residue 2178 THR Chi-restraints excluded: chain X residue 2226 CYS Chi-restraints excluded: chain X residue 2234 GLN Chi-restraints excluded: chain X residue 2236 TRP Chi-restraints excluded: chain X residue 2263 VAL Chi-restraints excluded: chain X residue 2283 PHE Chi-restraints excluded: chain X residue 2285 ASP Chi-restraints excluded: chain X residue 2377 LEU Chi-restraints excluded: chain X residue 2407 GLU Chi-restraints excluded: chain X residue 2426 TYR Chi-restraints excluded: chain X residue 2440 MET Chi-restraints excluded: chain X residue 2547 CYS Chi-restraints excluded: chain X residue 2554 TYR Chi-restraints excluded: chain X residue 2568 GLN Chi-restraints excluded: chain X residue 2601 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 0.0050 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5414 Z= 0.191 Angle : 0.946 14.807 7269 Z= 0.486 Chirality : 0.047 0.271 738 Planarity : 0.005 0.050 938 Dihedral : 7.728 39.957 693 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 20.63 % Favored : 79.21 % Rotamer: Outliers : 3.74 % Allowed : 21.56 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.31), residues: 635 helix: 0.37 (0.30), residues: 276 sheet: None (None), residues: 0 loop : -3.72 (0.28), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP X2144 HIS 0.006 0.001 HIS X2322 PHE 0.016 0.001 PHE X2066 TYR 0.028 0.001 TYR X2325 ARG 0.008 0.001 ARG X2371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 46 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 2065 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8263 (mp0) REVERT: X 2114 MET cc_start: 0.8853 (mpp) cc_final: 0.8643 (pmm) REVERT: X 2245 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8988 (mm-30) REVERT: X 2424 MET cc_start: 0.9476 (mtm) cc_final: 0.9058 (mtp) REVERT: X 2511 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8871 (tm-30) REVERT: X 2517 PHE cc_start: 0.8726 (t80) cc_final: 0.8085 (t80) REVERT: X 2526 ASP cc_start: 0.9374 (m-30) cc_final: 0.9128 (p0) REVERT: X 2555 LYS cc_start: 0.9743 (pptt) cc_final: 0.9502 (pptt) REVERT: X 2601 CYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5364 (p) outliers start: 22 outliers final: 19 residues processed: 64 average time/residue: 0.2161 time to fit residues: 17.6437 Evaluate side-chains 67 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 2012 CYS Chi-restraints excluded: chain X residue 2016 THR Chi-restraints excluded: chain X residue 2041 ILE Chi-restraints excluded: chain X residue 2066 PHE Chi-restraints excluded: chain X residue 2140 LYS Chi-restraints excluded: chain X residue 2178 THR Chi-restraints excluded: chain X residue 2226 CYS Chi-restraints excluded: chain X residue 2234 GLN Chi-restraints excluded: chain X residue 2236 TRP Chi-restraints excluded: chain X residue 2263 VAL Chi-restraints excluded: chain X residue 2283 PHE Chi-restraints excluded: chain X residue 2285 ASP Chi-restraints excluded: chain X residue 2377 LEU Chi-restraints excluded: chain X residue 2407 GLU Chi-restraints excluded: chain X residue 2426 TYR Chi-restraints excluded: chain X residue 2440 MET Chi-restraints excluded: chain X residue 2547 CYS Chi-restraints excluded: chain X residue 2554 TYR Chi-restraints excluded: chain X residue 2568 GLN Chi-restraints excluded: chain X residue 2601 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.0980 chunk 50 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2529 ASN X2582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.065140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.051742 restraints weight = 37203.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.054335 restraints weight = 28583.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.054660 restraints weight = 20069.994| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5414 Z= 0.186 Angle : 0.931 14.396 7269 Z= 0.477 Chirality : 0.047 0.279 738 Planarity : 0.005 0.051 938 Dihedral : 7.501 39.784 693 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 20.63 % Favored : 79.21 % Rotamer: Outliers : 2.89 % Allowed : 22.41 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.32), residues: 635 helix: 0.61 (0.30), residues: 270 sheet: None (None), residues: 0 loop : -3.60 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP X2144 HIS 0.006 0.001 HIS X2322 PHE 0.017 0.001 PHE X2066 TYR 0.024 0.001 TYR X2325 ARG 0.004 0.000 ARG X2371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1590.39 seconds wall clock time: 29 minutes 55.94 seconds (1795.94 seconds total)