Starting phenix.real_space_refine on Mon Jun 24 13:46:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbi_38219/06_2024/8xbi_38219_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbi_38219/06_2024/8xbi_38219.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbi_38219/06_2024/8xbi_38219_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbi_38219/06_2024/8xbi_38219_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbi_38219/06_2024/8xbi_38219_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbi_38219/06_2024/8xbi_38219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbi_38219/06_2024/8xbi_38219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbi_38219/06_2024/8xbi_38219_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbi_38219/06_2024/8xbi_38219_updated.pdb" } resolution = 3.06 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 ------------------------------------------------------------------------------- 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= -0.028 sd= 0.435 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 22 5.16 5 C 1641 2.51 5 N 399 2.21 5 O 404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 2467 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2424 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'KW3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.04, per 1000 atoms: 0.83 Number of scatterers: 2467 At special positions: 0 Unit cell: (64.55, 73.587, 77.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 1 15.00 O 404 8.00 N 399 7.00 C 1641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 299 " distance=2.04 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 204 " distance=2.08 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: 0.99 Conformation dependent library (CDL) restraints added in 405.0 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 0 sheets defined 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'R' and resid 51 through 81 Processing helix chain 'R' and resid 88 through 116 Proline residue: R 108 - end of helix Processing helix chain 'R' and resid 124 through 156 removed outlier: 3.552A pdb=" N TYR R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 196 removed outlier: 3.702A pdb=" N LYS R 195 " --> pdb=" O ILE R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 251 Processing helix chain 'R' and resid 260 through 293 Proline residue: R 281 - end of helix removed outlier: 3.919A pdb=" N PHE R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 330 removed outlier: 4.186A pdb=" N ILE R 304 " --> pdb=" O TYR R 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS R 321 " --> pdb=" O SER R 317 " (cutoff:3.500A) Proline residue: R 324 - end of helix removed outlier: 3.641A pdb=" N TYR R 327 " --> pdb=" O ASP R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 341 186 hydrogen bonds defined for protein. 558 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: 0.64 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 623 1.33 - 1.45: 447 1.45 - 1.58: 1417 1.58 - 1.71: 2 1.71 - 1.83: 34 Bond restraints: 2523 Sorted by residual: bond pdb=" C ALA R 265 " pdb=" O ALA R 265 " ideal model delta sigma weight residual 1.237 1.284 -0.047 1.17e-02 7.31e+03 1.61e+01 bond pdb=" N ILE R 82 " pdb=" CA ILE R 82 " ideal model delta sigma weight residual 1.459 1.491 -0.033 9.10e-03 1.21e+04 1.28e+01 bond pdb=" C ILE R 270 " pdb=" O ILE R 270 " ideal model delta sigma weight residual 1.237 1.276 -0.040 1.13e-02 7.83e+03 1.23e+01 bond pdb=" C6 KW3 R 401 " pdb=" O2 KW3 R 401 " ideal model delta sigma weight residual 1.396 1.329 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C4 KW3 R 401 " pdb=" O6 KW3 R 401 " ideal model delta sigma weight residual 1.399 1.465 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 2518 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.91: 35 105.91 - 112.99: 1369 112.99 - 120.08: 1072 120.08 - 127.17: 908 127.17 - 134.26: 23 Bond angle restraints: 3407 Sorted by residual: angle pdb=" O GLN R 161 " pdb=" C GLN R 161 " pdb=" N GLN R 162 " ideal model delta sigma weight residual 121.76 126.04 -4.28 1.15e+00 7.56e-01 1.39e+01 angle pdb=" C20 KW3 R 401 " pdb=" O5 KW3 R 401 " pdb=" C21 KW3 R 401 " ideal model delta sigma weight residual 109.47 120.64 -11.17 3.00e+00 1.11e-01 1.39e+01 angle pdb=" O7 KW3 R 401 " pdb=" P1 KW3 R 401 " pdb=" O8 KW3 R 401 " ideal model delta sigma weight residual 109.47 120.36 -10.89 3.00e+00 1.11e-01 1.32e+01 angle pdb=" N GLU R 303 " pdb=" CA GLU R 303 " pdb=" CB GLU R 303 " ideal model delta sigma weight residual 110.16 115.17 -5.01 1.48e+00 4.57e-01 1.14e+01 angle pdb=" CD LYS R 254 " pdb=" CE LYS R 254 " pdb=" NZ LYS R 254 " ideal model delta sigma weight residual 111.90 101.29 10.61 3.20e+00 9.77e-02 1.10e+01 ... (remaining 3402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.43: 1271 13.43 - 26.86: 156 26.86 - 40.29: 49 40.29 - 53.72: 9 53.72 - 67.15: 6 Dihedral angle restraints: 1491 sinusoidal: 609 harmonic: 882 Sorted by residual: dihedral pdb=" CA ILE R 156 " pdb=" C ILE R 156 " pdb=" N ASN R 157 " pdb=" CA ASN R 157 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLN R 162 " pdb=" C GLN R 162 " pdb=" N ARG R 163 " pdb=" CA ARG R 163 " ideal model delta harmonic sigma weight residual 180.00 163.59 16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG R 208 " pdb=" CD ARG R 208 " pdb=" NE ARG R 208 " pdb=" CZ ARG R 208 " ideal model delta sinusoidal sigma weight residual -180.00 -137.72 -42.28 2 1.50e+01 4.44e-03 9.65e+00 ... (remaining 1488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 162 0.038 - 0.075: 119 0.075 - 0.113: 68 0.113 - 0.150: 42 0.150 - 0.188: 10 Chirality restraints: 401 Sorted by residual: chirality pdb=" CA ILE R 148 " pdb=" N ILE R 148 " pdb=" C ILE R 148 " pdb=" CB ILE R 148 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA ILE R 156 " pdb=" N ILE R 156 " pdb=" C ILE R 156 " pdb=" CB ILE R 156 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA ILE R 98 " pdb=" N ILE R 98 " pdb=" C ILE R 98 " pdb=" CB ILE R 98 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 398 not shown) Planarity restraints: 399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 269 " 0.039 2.00e-02 2.50e+03 2.60e-02 1.19e+01 pdb=" CG PHE R 269 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE R 269 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 269 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE R 269 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE R 269 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 269 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 238 " 0.032 2.00e-02 2.50e+03 2.31e-02 1.07e+01 pdb=" CG TYR R 238 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR R 238 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR R 238 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR R 238 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR R 238 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR R 238 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR R 238 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 279 " 0.024 2.00e-02 2.50e+03 2.21e-02 8.53e+00 pdb=" CG PHE R 279 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE R 279 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 279 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE R 279 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE R 279 " 0.029 2.00e-02 2.50e+03 pdb=" CZ PHE R 279 " 0.009 2.00e-02 2.50e+03 ... (remaining 396 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 188 2.76 - 3.29: 2786 3.29 - 3.83: 3996 3.83 - 4.36: 4798 4.36 - 4.90: 8164 Nonbonded interactions: 19932 Sorted by model distance: nonbonded pdb=" OH TYR R 282 " pdb=" NH2 ARG R 286 " model vdw 2.221 2.520 nonbonded pdb=" O LYS R 155 " pdb=" OG SER R 159 " model vdw 2.232 2.440 nonbonded pdb=" OG SER R 54 " pdb=" O HIS R 114 " model vdw 2.239 2.440 nonbonded pdb=" OG SER R 331 " pdb=" OD1 ASN R 333 " model vdw 2.276 2.440 nonbonded pdb=" O VAL R 78 " pdb=" ND1 HIS R 83 " model vdw 2.339 2.520 ... (remaining 19927 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.010 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.070 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.013 0.067 2523 Z= 0.828 Angle : 1.255 11.173 3407 Z= 0.884 Chirality : 0.071 0.188 401 Planarity : 0.006 0.027 399 Dihedral : 13.633 67.150 915 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.45), residues: 296 helix: 2.03 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -1.99 (0.66), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.006 TRP R 179 HIS 0.007 0.002 HIS R 206 PHE 0.053 0.007 PHE R 269 TYR 0.045 0.008 TYR R 238 ARG 0.012 0.002 ARG R 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: R 247 ARG cc_start: 0.7415 (ptm-80) cc_final: 0.6991 (tpp-160) REVERT: R 251 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6919 (ptt180) REVERT: R 303 GLU cc_start: 0.7252 (pm20) cc_final: 0.6944 (pt0) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1816 time to fit residues: 13.6586 Evaluate side-chains 48 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 95 ASN ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2523 Z= 0.146 Angle : 0.509 5.327 3407 Z= 0.277 Chirality : 0.038 0.139 401 Planarity : 0.003 0.028 399 Dihedral : 8.767 77.217 340 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.82 % Allowed : 10.55 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.47), residues: 296 helix: 2.55 (0.32), residues: 238 sheet: None (None), residues: 0 loop : -2.04 (0.66), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 228 HIS 0.003 0.001 HIS R 206 PHE 0.010 0.001 PHE R 227 TYR 0.010 0.001 TYR R 139 ARG 0.003 0.000 ARG R 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.252 Fit side-chains REVERT: R 247 ARG cc_start: 0.7398 (ptm-80) cc_final: 0.6972 (tpp-160) REVERT: R 251 ARG cc_start: 0.7097 (mtm110) cc_final: 0.6625 (ptt180) REVERT: R 303 GLU cc_start: 0.7107 (pm20) cc_final: 0.6858 (tt0) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.1616 time to fit residues: 10.8401 Evaluate side-chains 52 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 317 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.0770 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 95 ASN ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2523 Z= 0.135 Angle : 0.473 5.131 3407 Z= 0.260 Chirality : 0.037 0.130 401 Planarity : 0.003 0.027 399 Dihedral : 8.298 76.847 340 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.09 % Allowed : 13.09 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.47), residues: 296 helix: 2.56 (0.32), residues: 238 sheet: None (None), residues: 0 loop : -2.09 (0.64), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 301 HIS 0.003 0.001 HIS R 206 PHE 0.010 0.001 PHE R 227 TYR 0.011 0.001 TYR R 139 ARG 0.004 0.000 ARG R 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.237 Fit side-chains REVERT: R 51 LYS cc_start: 0.7112 (mppt) cc_final: 0.6396 (tttt) REVERT: R 247 ARG cc_start: 0.7287 (ptm-80) cc_final: 0.6817 (tpp-160) REVERT: R 251 ARG cc_start: 0.7120 (mtm110) cc_final: 0.6653 (ptt180) outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.1689 time to fit residues: 11.2269 Evaluate side-chains 55 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 0.0050 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2523 Z= 0.205 Angle : 0.535 5.070 3407 Z= 0.287 Chirality : 0.039 0.135 401 Planarity : 0.004 0.030 399 Dihedral : 8.528 87.116 340 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.91 % Allowed : 14.91 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.47), residues: 296 helix: 2.21 (0.32), residues: 233 sheet: None (None), residues: 0 loop : -2.03 (0.62), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 228 HIS 0.004 0.001 HIS R 306 PHE 0.017 0.002 PHE R 227 TYR 0.013 0.002 TYR R 139 ARG 0.007 0.001 ARG R 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: R 51 LYS cc_start: 0.6984 (mppt) cc_final: 0.6418 (tttt) REVERT: R 247 ARG cc_start: 0.7416 (ptm-80) cc_final: 0.7032 (tpp-160) REVERT: R 251 ARG cc_start: 0.7101 (mtm110) cc_final: 0.6603 (ptt180) REVERT: R 318 PHE cc_start: 0.7245 (t80) cc_final: 0.6879 (t80) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.1532 time to fit residues: 11.2231 Evaluate side-chains 60 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 317 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2523 Z= 0.143 Angle : 0.488 5.050 3407 Z= 0.262 Chirality : 0.038 0.156 401 Planarity : 0.003 0.023 399 Dihedral : 8.256 87.751 340 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.82 % Allowed : 16.73 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.47), residues: 296 helix: 2.31 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -2.03 (0.62), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 228 HIS 0.003 0.001 HIS R 206 PHE 0.012 0.001 PHE R 227 TYR 0.015 0.001 TYR R 282 ARG 0.004 0.000 ARG R 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.277 Fit side-chains REVERT: R 48 MET cc_start: 0.5363 (pmm) cc_final: 0.4761 (ptp) REVERT: R 51 LYS cc_start: 0.6943 (mppt) cc_final: 0.6446 (tttt) REVERT: R 247 ARG cc_start: 0.7315 (ptm-80) cc_final: 0.6824 (tpp-160) REVERT: R 251 ARG cc_start: 0.7128 (mtm110) cc_final: 0.6669 (ptt180) REVERT: R 303 GLU cc_start: 0.7865 (tt0) cc_final: 0.7167 (pm20) REVERT: R 318 PHE cc_start: 0.7257 (t80) cc_final: 0.6894 (t80) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.1540 time to fit residues: 10.8786 Evaluate side-chains 61 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 317 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 118 ASN ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2523 Z= 0.276 Angle : 0.619 6.506 3407 Z= 0.324 Chirality : 0.043 0.168 401 Planarity : 0.004 0.048 399 Dihedral : 8.750 92.132 340 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.27 % Allowed : 18.18 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.46), residues: 296 helix: 1.63 (0.32), residues: 232 sheet: None (None), residues: 0 loop : -1.61 (0.68), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 228 HIS 0.004 0.001 HIS R 306 PHE 0.021 0.002 PHE R 227 TYR 0.025 0.002 TYR R 282 ARG 0.005 0.001 ARG R 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.270 Fit side-chains REVERT: R 51 LYS cc_start: 0.7189 (mppt) cc_final: 0.6747 (tttt) REVERT: R 247 ARG cc_start: 0.7347 (ptm-80) cc_final: 0.6947 (tpp-160) REVERT: R 251 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6756 (ptt180) REVERT: R 318 PHE cc_start: 0.7365 (t80) cc_final: 0.7014 (t80) outliers start: 9 outliers final: 5 residues processed: 59 average time/residue: 0.1586 time to fit residues: 11.0986 Evaluate side-chains 57 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 317 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2523 Z= 0.200 Angle : 0.542 5.470 3407 Z= 0.290 Chirality : 0.040 0.146 401 Planarity : 0.003 0.022 399 Dihedral : 8.534 91.760 340 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.27 % Allowed : 17.82 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.47), residues: 296 helix: 1.76 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.91 (0.64), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 228 HIS 0.003 0.001 HIS R 206 PHE 0.015 0.002 PHE R 227 TYR 0.018 0.002 TYR R 282 ARG 0.005 0.001 ARG R 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.318 Fit side-chains REVERT: R 51 LYS cc_start: 0.7199 (mppt) cc_final: 0.6743 (tttt) REVERT: R 247 ARG cc_start: 0.7347 (ptm-80) cc_final: 0.6940 (tpp-160) REVERT: R 251 ARG cc_start: 0.7299 (mtm110) cc_final: 0.6960 (mtp180) REVERT: R 318 PHE cc_start: 0.7353 (t80) cc_final: 0.6995 (t80) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.1530 time to fit residues: 10.8003 Evaluate side-chains 64 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 317 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 23 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2523 Z= 0.149 Angle : 0.497 5.324 3407 Z= 0.265 Chirality : 0.039 0.162 401 Planarity : 0.003 0.021 399 Dihedral : 8.247 92.325 340 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.18 % Allowed : 20.73 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.48), residues: 296 helix: 2.12 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.90 (0.64), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 301 HIS 0.004 0.001 HIS R 206 PHE 0.011 0.001 PHE R 227 TYR 0.015 0.001 TYR R 282 ARG 0.004 0.000 ARG R 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.282 Fit side-chains REVERT: R 48 MET cc_start: 0.5140 (pmm) cc_final: 0.4742 (ptp) REVERT: R 51 LYS cc_start: 0.7211 (mppt) cc_final: 0.6761 (tttt) REVERT: R 247 ARG cc_start: 0.7217 (ptm-80) cc_final: 0.6802 (tpp-160) REVERT: R 251 ARG cc_start: 0.7312 (mtm110) cc_final: 0.7003 (mtp180) REVERT: R 282 TYR cc_start: 0.8404 (t80) cc_final: 0.8141 (t80) REVERT: R 318 PHE cc_start: 0.7178 (t80) cc_final: 0.6823 (t80) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.1576 time to fit residues: 11.9946 Evaluate side-chains 63 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 317 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2523 Z= 0.155 Angle : 0.492 5.010 3407 Z= 0.265 Chirality : 0.039 0.172 401 Planarity : 0.003 0.022 399 Dihedral : 8.157 91.585 340 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.18 % Allowed : 20.73 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.48), residues: 296 helix: 2.18 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.90 (0.64), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 120 HIS 0.003 0.001 HIS R 206 PHE 0.011 0.001 PHE R 227 TYR 0.014 0.001 TYR R 139 ARG 0.004 0.000 ARG R 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: R 48 MET cc_start: 0.5441 (pmm) cc_final: 0.5166 (ptp) REVERT: R 51 LYS cc_start: 0.7213 (mppt) cc_final: 0.6761 (tttt) REVERT: R 247 ARG cc_start: 0.7271 (ptm-80) cc_final: 0.6820 (tpp-160) REVERT: R 251 ARG cc_start: 0.7294 (mtm110) cc_final: 0.7005 (ttp80) REVERT: R 282 TYR cc_start: 0.8470 (t80) cc_final: 0.8216 (t80) REVERT: R 318 PHE cc_start: 0.7179 (t80) cc_final: 0.6820 (t80) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.1636 time to fit residues: 11.1315 Evaluate side-chains 61 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 317 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2523 Z= 0.210 Angle : 0.553 5.653 3407 Z= 0.295 Chirality : 0.040 0.170 401 Planarity : 0.003 0.027 399 Dihedral : 8.336 91.747 340 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.55 % Allowed : 21.09 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.48), residues: 296 helix: 1.95 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -1.84 (0.67), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 120 HIS 0.004 0.001 HIS R 306 PHE 0.016 0.002 PHE R 227 TYR 0.013 0.002 TYR R 282 ARG 0.005 0.001 ARG R 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.278 Fit side-chains REVERT: R 48 MET cc_start: 0.5641 (pmm) cc_final: 0.5425 (ptp) REVERT: R 51 LYS cc_start: 0.7322 (mppt) cc_final: 0.6986 (tttt) REVERT: R 247 ARG cc_start: 0.7348 (ptm-80) cc_final: 0.6982 (tpp-160) REVERT: R 251 ARG cc_start: 0.7261 (mtm110) cc_final: 0.6950 (mtp180) REVERT: R 318 PHE cc_start: 0.7374 (t80) cc_final: 0.7022 (t80) outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.1584 time to fit residues: 11.0117 Evaluate side-chains 59 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 159 SER Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 317 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 0.0050 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 HIS ** 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 = 0.4197 r_free = 0.4197 target = 0.204680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.170057 restraints weight = 2683.512| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.70 r_work: 0.3689 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2523 Z= 0.150 Angle : 0.489 4.904 3407 Z= 0.267 Chirality : 0.039 0.168 401 Planarity : 0.003 0.021 399 Dihedral : 8.071 90.607 340 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.82 % Allowed : 21.45 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.48), residues: 296 helix: 2.31 (0.33), residues: 232 sheet: None (None), residues: 0 loop : -1.77 (0.66), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 120 HIS 0.004 0.001 HIS R 206 PHE 0.011 0.001 PHE R 227 TYR 0.017 0.001 TYR R 282 ARG 0.003 0.000 ARG R 286 =============================================================================== Job complete usr+sys time: 895.41 seconds wall clock time: 16 minutes 44.49 seconds (1004.49 seconds total)