Starting phenix.real_space_refine (version: dev) on Mon Apr 4 13:09:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/04_2022/7nnh_12477.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/04_2022/7nnh_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_12477/04_2022/7nnh_12477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/04_2022/7nnh_12477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/04_2022/7nnh_12477.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnh_12477/04_2022/7nnh_12477.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "X PHE 2428": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 18, 'CIS': 19, 'TRANS': 598, 'PCIS': 1} Time building chain proxies: 3.48, per 1000 atoms: 0.66 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: 2.39 Conformation dependent library (CDL) restraints added in 735.7 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: 0.15 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: 1.22 Time building geometry restraints manager: 2.60 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 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 angle pdb=" N ASP X2543 " pdb=" CA ASP X2543 " pdb=" C ASP X2543 " ideal model delta sigma weight residual 114.62 107.69 6.93 1.14e+00 7.69e-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 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. 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: 3.020 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: 0.000 Extract box with map and model: 16.950 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 19.540 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 1.269 13.978 7269 Z= 0.735 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 : 34.87 Ramachandran Plot: Outliers : 0.47 % Allowed : 22.99 % Favored : 76.54 % Rotamer Outliers : 0.34 % 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 *********************** 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 : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.2189 time to fit residues: 18.3629 Evaluate side-chains 42 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9546 ------------------------------------------------------------------------------- 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: 0.2980 chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 0.0870 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.0040 chunk 36 optimal weight: 0.0170 chunk 57 optimal weight: 0.7980 overall best weight: 0.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X2083 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 5414 Z= 0.214 Angle : 1.106 19.158 7269 Z= 0.529 Chirality : 0.049 0.214 738 Planarity : 0.006 0.051 938 Dihedral : 9.142 57.559 693 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.79 % Allowed : 20.00 % Favored : 79.21 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.76 % 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: -2.99 (0.30), residues: 635 helix: 0.12 (0.30), residues: 269 sheet: None (None), residues: 0 loop : -3.93 (0.27), residues: 366 *********************** 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 62 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.2148 time to fit residues: 16.2472 Evaluate side-chains 44 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0603 time to fit residues: 1.2646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X2047 GLN ** X2083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X2505 GLN 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: 0.7999 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 5414 Z= 0.228 Angle : 1.057 19.093 7269 Z= 0.509 Chirality : 0.046 0.204 738 Planarity : 0.005 0.051 938 Dihedral : 8.553 40.745 693 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 32.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 20.63 % Favored : 79.21 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.59 % Twisted Proline : 5.26 % Twisted General : 0.97 % 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: -2.93 (0.31), residues: 635 helix: 0.14 (0.30), residues: 271 sheet: None (None), residues: 0 loop : -3.88 (0.27), residues: 364 *********************** 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 62 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.2004 time to fit residues: 15.9300 Evaluate side-chains 49 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0968 time to fit residues: 2.1954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 27 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- 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** ** X2505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2568 GLN ** X2570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3054 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= 0.220 Angle : 1.053 19.694 7269 Z= 0.500 Chirality : 0.046 0.202 738 Planarity : 0.005 0.051 938 Dihedral : 8.281 35.702 693 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 31.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 21.10 % Favored : 78.58 % Rotamer Outliers : 1.87 % 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: -2.98 (0.30), residues: 635 helix: 0.04 (0.30), residues: 271 sheet: None (None), residues: 0 loop : -3.85 (0.27), residues: 364 *********************** 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 53 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 0.1955 time to fit residues: 13.5047 Evaluate side-chains 45 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0886 time to fit residues: 2.0576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** X2505 GLN ** X2556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3508 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= 0.188 Angle : 1.030 19.556 7269 Z= 0.487 Chirality : 0.045 0.199 738 Planarity : 0.005 0.051 938 Dihedral : 8.043 35.570 693 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 27.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 20.94 % Favored : 78.74 % Rotamer Outliers : 1.53 % 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: -2.83 (0.31), residues: 635 helix: 0.16 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.73 (0.27), residues: 368 *********************** 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 54 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 54 average time/residue: 0.2454 time to fit residues: 16.6765 Evaluate side-chains 43 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0777 time to fit residues: 1.4601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X2047 GLN ** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X2597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 5414 Z= 0.334 Angle : 1.100 20.119 7269 Z= 0.544 Chirality : 0.048 0.204 738 Planarity : 0.006 0.048 938 Dihedral : 8.501 35.938 693 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 43.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 22.36 % Favored : 77.48 % Rotamer Outliers : 1.53 % 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: -3.05 (0.30), residues: 635 helix: -0.06 (0.30), residues: 271 sheet: None (None), residues: 0 loop : -3.86 (0.27), residues: 364 *********************** 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 50 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 49 average time/residue: 0.2158 time to fit residues: 13.8358 Evaluate side-chains 43 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1228 time to fit residues: 1.7951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 ** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X2505 GLN X2529 ASN ** X2582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3902 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= 0.200 Angle : 1.063 20.765 7269 Z= 0.505 Chirality : 0.046 0.187 738 Planarity : 0.005 0.051 938 Dihedral : 8.164 33.412 693 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 30.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 21.10 % Favored : 78.74 % Rotamer Outliers : 1.19 % 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: -2.92 (0.30), residues: 635 helix: 0.07 (0.30), residues: 264 sheet: None (None), residues: 0 loop : -3.73 (0.27), residues: 371 *********************** 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 53 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 53 average time/residue: 0.2087 time to fit residues: 14.3753 Evaluate side-chains 42 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0575 time to fit residues: 1.1071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** X2269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 5414 Z= 0.208 Angle : 1.067 20.145 7269 Z= 0.505 Chirality : 0.046 0.225 738 Planarity : 0.005 0.050 938 Dihedral : 8.023 33.518 693 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 32.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 21.73 % Favored : 78.11 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.92 % Twisted Proline : 5.26 % Twisted General : 0.32 % 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: -2.79 (0.31), residues: 635 helix: 0.25 (0.31), residues: 259 sheet: None (None), residues: 0 loop : -3.68 (0.28), residues: 376 *********************** 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 58 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 54 average time/residue: 0.2168 time to fit residues: 15.1444 Evaluate side-chains 50 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1337 time to fit residues: 2.3359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 36 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** ** X2269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2505 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: 0.7948 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 5414 Z= 0.201 Angle : 1.073 19.876 7269 Z= 0.505 Chirality : 0.047 0.249 738 Planarity : 0.005 0.051 938 Dihedral : 7.921 35.666 693 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 28.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 20.94 % Favored : 78.90 % Rotamer Outliers : 0.68 % 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: -2.78 (0.31), residues: 635 helix: 0.25 (0.30), residues: 262 sheet: None (None), residues: 0 loop : -3.68 (0.28), residues: 373 *********************** 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 49 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.2285 time to fit residues: 14.1767 Evaluate side-chains 44 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0865 time to fit residues: 1.2562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- 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** ** X2269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2505 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: 0.7985 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 5414 Z= 0.212 Angle : 1.090 18.948 7269 Z= 0.518 Chirality : 0.048 0.227 738 Planarity : 0.005 0.050 938 Dihedral : 7.878 37.191 693 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 30.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 22.05 % Favored : 77.80 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.76 % 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: -2.84 (0.31), residues: 635 helix: 0.15 (0.30), residues: 268 sheet: None (None), residues: 0 loop : -3.75 (0.28), residues: 367 ********************** 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 44 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.2194 time to fit residues: 12.4542 Evaluate side-chains 42 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2203 time to fit residues: 1.4741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** ** X2269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2582 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 = 0.3735 r_free = 0.3735 target = 0.062985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.049541 restraints weight = 38053.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.050328 restraints weight = 28127.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.050845 restraints weight = 25038.279| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 5414 Z= 0.197 Angle : 1.078 18.490 7269 Z= 0.509 Chirality : 0.047 0.244 738 Planarity : 0.005 0.051 938 Dihedral : 7.769 37.475 693 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 27.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 21.42 % Favored : 78.43 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 2.76 % 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: -2.67 (0.31), residues: 635 helix: 0.35 (0.30), residues: 262 sheet: None (None), residues: 0 loop : -3.63 (0.28), residues: 373 =============================================================================== Job complete usr+sys time: 1486.13 seconds wall clock time: 27 minutes 53.86 seconds (1673.86 seconds total)