Starting phenix.real_space_refine on Sat Mar 16 14:37:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/03_2024/8t2s_40986_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/03_2024/8t2s_40986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/03_2024/8t2s_40986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/03_2024/8t2s_40986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/03_2024/8t2s_40986_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/03_2024/8t2s_40986_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 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: 6 Type Number sf(0) Gaussians Ca 11 9.91 5 P 551 5.49 5 S 21 5.16 5 C 7283 2.51 5 N 2764 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D ASP 265": "OD1" <-> "OD2" Residue "D ASP 280": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14998 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3146 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 10, 'TRANS': 378} Chain breaks: 2 Chain: "B" Number of atoms: 11839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 11839 Classifications: {'RNA': 551} Modifications used: {'rna2p_pur': 46, 'rna2p_pyr': 17, 'rna3p_pur': 283, 'rna3p_pyr': 205} Link IDs: {'rna2p': 62, 'rna3p': 488} Chain breaks: 6 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CA': 11, 'NH4': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Time building chain proxies: 9.10, per 1000 atoms: 0.61 Number of scatterers: 14998 At special positions: 0 Unit cell: (110.564, 136.728, 160.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 11 19.99 S 21 16.00 P 551 15.00 O 4368 8.00 N 2764 7.00 C 7283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.12 Conformation dependent library (CDL) restraints added in 641.0 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 57.3% alpha, 5.7% beta 181 base pairs and 323 stacking pairs defined. Time for finding SS restraints: 8.62 Creating SS restraints... Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 40 through 56 removed outlier: 5.712A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 95 Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 119 through 132 Processing helix chain 'D' and resid 145 through 148 No H-bonds generated for 'chain 'D' and resid 145 through 148' Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.538A pdb=" N VAL D 171 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 172 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 173 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR D 174 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 175 " --> pdb=" O ARG D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 216 removed outlier: 3.863A pdb=" N GLU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 Processing helix chain 'D' and resid 292 through 305 removed outlier: 3.577A pdb=" N LYS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 329 Processing helix chain 'D' and resid 338 through 360 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 377 through 385 Processing helix chain 'D' and resid 390 through 395 removed outlier: 3.550A pdb=" N ASN D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 416 through 423 Processing sheet with id= A, first strand: chain 'D' and resid 136 through 141 removed outlier: 4.251A pdb=" N CYS D 228 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 275 through 279 147 hydrogen bonds defined for protein. 429 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 447 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 181 basepair parallelities 323 stacking parallelities Total time for adding SS restraints: 7.73 Time building geometry restraints manager: 8.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1521 1.32 - 1.45: 7659 1.45 - 1.57: 6151 1.57 - 1.69: 1096 1.69 - 1.82: 35 Bond restraints: 16462 Sorted by residual: bond pdb=" C THR D 99 " pdb=" N PRO D 100 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.28e-02 6.10e+03 4.24e+00 bond pdb=" CG GLN D 63 " pdb=" CD GLN D 63 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 3.98e+00 bond pdb=" CB GLN D 63 " pdb=" CG GLN D 63 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.27e+00 bond pdb=" C3' G B 369 " pdb=" O3' G B 369 " ideal model delta sigma weight residual 1.427 1.453 -0.026 1.50e-02 4.44e+03 2.98e+00 bond pdb=" CB ASP D 226 " pdb=" CG ASP D 226 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.93e+00 ... (remaining 16457 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.88: 3019 105.88 - 113.65: 10149 113.65 - 121.41: 7657 121.41 - 129.18: 3707 129.18 - 136.94: 432 Bond angle restraints: 24964 Sorted by residual: angle pdb=" CA MET D 7 " pdb=" CB MET D 7 " pdb=" CG MET D 7 " ideal model delta sigma weight residual 114.10 124.56 -10.46 2.00e+00 2.50e-01 2.73e+01 angle pdb=" CA GLU D 235 " pdb=" CB GLU D 235 " pdb=" CG GLU D 235 " ideal model delta sigma weight residual 114.10 124.39 -10.29 2.00e+00 2.50e-01 2.65e+01 angle pdb=" C3' G B 369 " pdb=" O3' G B 369 " pdb=" P A B 370 " ideal model delta sigma weight residual 120.20 127.87 -7.67 1.50e+00 4.44e-01 2.62e+01 angle pdb=" C3' A B 551 " pdb=" O3' A B 551 " pdb=" P U B 552 " ideal model delta sigma weight residual 120.20 127.62 -7.42 1.50e+00 4.44e-01 2.44e+01 angle pdb=" C3' A B 67 " pdb=" O3' A B 67 " pdb=" P U B 68 " ideal model delta sigma weight residual 120.20 127.32 -7.12 1.50e+00 4.44e-01 2.25e+01 ... (remaining 24959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 8923 35.46 - 70.92: 1328 70.92 - 106.37: 142 106.37 - 141.83: 7 141.83 - 177.29: 10 Dihedral angle restraints: 10410 sinusoidal: 9280 harmonic: 1130 Sorted by residual: dihedral pdb=" O4' C B 581 " pdb=" C1' C B 581 " pdb=" N1 C B 581 " pdb=" C2 C B 581 " ideal model delta sinusoidal sigma weight residual -160.00 12.10 -172.10 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U B 172 " pdb=" C1' U B 172 " pdb=" N1 U B 172 " pdb=" C2 U B 172 " ideal model delta sinusoidal sigma weight residual 200.00 31.97 168.03 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' C B 439 " pdb=" C1' C B 439 " pdb=" N1 C B 439 " pdb=" C2 C B 439 " ideal model delta sinusoidal sigma weight residual 200.00 43.48 156.52 1 1.50e+01 4.44e-03 8.18e+01 ... (remaining 10407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2939 0.068 - 0.135: 241 0.135 - 0.203: 25 0.203 - 0.271: 10 0.271 - 0.338: 8 Chirality restraints: 3223 Sorted by residual: chirality pdb=" C3' C B 206 " pdb=" C4' C B 206 " pdb=" O3' C B 206 " pdb=" C2' C B 206 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C3' G B 369 " pdb=" C4' G B 369 " pdb=" O3' G B 369 " pdb=" C2' G B 369 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C3' C B 39 " pdb=" C4' C B 39 " pdb=" O3' C B 39 " pdb=" C2' C B 39 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 3220 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 185 " -0.043 2.00e-02 2.50e+03 1.91e-02 1.01e+01 pdb=" N9 A B 185 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A B 185 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 185 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A B 185 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A B 185 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A B 185 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A B 185 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A B 185 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B 185 " 0.013 2.00e-02 2.50e+03 pdb=" C4 A B 185 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 266 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO D 267 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 267 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 267 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 175 " 0.033 2.00e-02 2.50e+03 1.66e-02 6.18e+00 pdb=" N1 U B 175 " -0.033 2.00e-02 2.50e+03 pdb=" C2 U B 175 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U B 175 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U B 175 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U B 175 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U B 175 " 0.011 2.00e-02 2.50e+03 pdb=" C5 U B 175 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U B 175 " -0.006 2.00e-02 2.50e+03 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2987 2.78 - 3.31: 12039 3.31 - 3.84: 33287 3.84 - 4.37: 38343 4.37 - 4.90: 49215 Nonbonded interactions: 135871 Sorted by model distance: nonbonded pdb=" OP2 A B 137 " pdb=" O2' A B 147 " model vdw 2.251 2.440 nonbonded pdb=" O2' G B 276 " pdb=" O4 U B 325 " model vdw 2.259 2.440 nonbonded pdb=" O2' G B 136 " pdb=" OP1 U B 148 " model vdw 2.277 2.440 nonbonded pdb=" OD1 ASN D 395 " pdb=" O2' A B -33 " model vdw 2.287 2.440 nonbonded pdb=" N2 G B 287 " pdb=" O2 C B 315 " model vdw 2.304 2.496 ... (remaining 135866 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 12.700 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 51.530 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 0.054 16462 Z= 0.232 Angle : 0.889 13.780 24964 Z= 0.433 Chirality : 0.042 0.338 3223 Planarity : 0.006 0.064 1096 Dihedral : 24.681 177.289 9682 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.04 % Allowed : 24.49 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.71 (0.36), residues: 383 helix: -1.32 (0.28), residues: 246 sheet: -1.07 (0.98), residues: 24 loop : -2.72 (0.45), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 357 HIS 0.008 0.002 HIS D 43 PHE 0.019 0.003 PHE D 89 TYR 0.019 0.002 TYR D 60 ARG 0.005 0.001 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.776 Fit side-chains REVERT: D 130 MET cc_start: 0.7844 (mtt) cc_final: 0.7623 (mtt) REVERT: D 236 MET cc_start: 0.7785 (ppp) cc_final: 0.7583 (ppp) REVERT: D 266 ARG cc_start: 0.8347 (mmt90) cc_final: 0.7959 (mmm-85) REVERT: D 406 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7592 (mppt) outliers start: 7 outliers final: 2 residues processed: 38 average time/residue: 1.5178 time to fit residues: 63.2843 Evaluate side-chains 29 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 166 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 16462 Z= 0.383 Angle : 0.700 7.570 24964 Z= 0.356 Chirality : 0.040 0.282 3223 Planarity : 0.005 0.041 1096 Dihedral : 24.616 174.939 8878 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.41 % Allowed : 19.53 % Favored : 74.05 % 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: -1.59 (0.39), residues: 383 helix: -0.23 (0.32), residues: 236 sheet: -1.47 (0.93), residues: 24 loop : -2.47 (0.49), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 357 HIS 0.005 0.001 HIS D 109 PHE 0.013 0.002 PHE D 146 TYR 0.024 0.002 TYR D 385 ARG 0.003 0.001 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 30 time to evaluate : 0.772 Fit side-chains REVERT: D 59 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7412 (mtmp) REVERT: D 251 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: D 347 ARG cc_start: 0.7561 (mtt-85) cc_final: 0.6941 (mmm-85) REVERT: D 364 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7356 (mm-40) REVERT: D 406 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7887 (mppt) outliers start: 22 outliers final: 10 residues processed: 48 average time/residue: 1.4384 time to fit residues: 75.7658 Evaluate side-chains 42 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 29 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 364 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 84 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 30.0000 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16462 Z= 0.254 Angle : 0.636 7.824 24964 Z= 0.326 Chirality : 0.036 0.290 3223 Planarity : 0.004 0.037 1096 Dihedral : 24.645 175.354 8878 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.54 % Allowed : 22.16 % Favored : 72.30 % 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: -0.92 (0.42), residues: 383 helix: 0.42 (0.34), residues: 236 sheet: -1.62 (0.89), residues: 24 loop : -2.40 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 357 HIS 0.003 0.001 HIS D 109 PHE 0.011 0.002 PHE D 89 TYR 0.021 0.001 TYR D 385 ARG 0.002 0.000 ARG D 351 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 30 time to evaluate : 0.752 Fit side-chains REVERT: D 59 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7298 (mtmp) REVERT: D 251 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: D 261 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7382 (mtpp) REVERT: D 280 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7559 (t0) REVERT: D 364 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7266 (mm-40) REVERT: D 406 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7915 (mppt) outliers start: 19 outliers final: 7 residues processed: 44 average time/residue: 1.3174 time to fit residues: 64.0173 Evaluate side-chains 41 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 29 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 80 optimal weight: 30.0000 chunk 24 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 16462 Z= 0.473 Angle : 0.748 7.686 24964 Z= 0.380 Chirality : 0.043 0.304 3223 Planarity : 0.005 0.037 1096 Dihedral : 24.594 173.229 8878 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 8.45 % Allowed : 22.16 % Favored : 69.39 % 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: -1.06 (0.41), residues: 383 helix: 0.31 (0.33), residues: 236 sheet: -1.76 (0.87), residues: 24 loop : -2.43 (0.49), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 357 HIS 0.006 0.001 HIS D 109 PHE 0.013 0.003 PHE D 146 TYR 0.025 0.002 TYR D 385 ARG 0.004 0.001 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 30 time to evaluate : 0.714 Fit side-chains REVERT: D 59 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7334 (mtmp) REVERT: D 162 ILE cc_start: 0.7888 (mm) cc_final: 0.7566 (mp) REVERT: D 247 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6951 (ttp80) REVERT: D 251 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: D 261 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7344 (mtpp) REVERT: D 266 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8068 (mmm-85) REVERT: D 280 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7502 (t0) REVERT: D 364 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7316 (mm-40) REVERT: D 388 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7092 (ptmm) REVERT: D 406 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7761 (mtpt) outliers start: 29 outliers final: 11 residues processed: 51 average time/residue: 1.4591 time to fit residues: 81.7499 Evaluate side-chains 47 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 28 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 388 LYS Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 407 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 22 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16462 Z= 0.373 Angle : 0.680 7.469 24964 Z= 0.347 Chirality : 0.040 0.290 3223 Planarity : 0.005 0.038 1096 Dihedral : 24.509 173.982 8878 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 8.75 % Allowed : 22.45 % Favored : 68.80 % 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: -0.88 (0.41), residues: 383 helix: 0.50 (0.34), residues: 236 sheet: -2.03 (0.86), residues: 24 loop : -2.38 (0.49), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 PHE 0.012 0.002 PHE D 146 TYR 0.023 0.002 TYR D 385 ARG 0.004 0.000 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 29 time to evaluate : 0.748 Fit side-chains REVERT: D 59 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7358 (mtmp) REVERT: D 96 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: D 162 ILE cc_start: 0.7897 (mm) cc_final: 0.7588 (mp) REVERT: D 247 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6925 (ttp80) REVERT: D 251 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: D 253 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8000 (mp) REVERT: D 261 LYS cc_start: 0.7887 (mtmm) cc_final: 0.7341 (mtpp) REVERT: D 266 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8053 (mmm-85) REVERT: D 280 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7537 (t0) REVERT: D 364 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7314 (mm-40) REVERT: D 406 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7761 (mtpt) REVERT: D 415 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8448 (p) outliers start: 30 outliers final: 12 residues processed: 51 average time/residue: 1.3636 time to fit residues: 76.2852 Evaluate side-chains 49 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 27 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 30.0000 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16462 Z= 0.283 Angle : 0.645 10.333 24964 Z= 0.329 Chirality : 0.037 0.294 3223 Planarity : 0.004 0.039 1096 Dihedral : 24.539 174.184 8878 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 7.58 % Allowed : 24.78 % Favored : 67.64 % 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: -0.65 (0.42), residues: 383 helix: 0.67 (0.34), residues: 236 sheet: -1.86 (0.88), residues: 24 loop : -2.28 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 PHE 0.010 0.002 PHE D 89 TYR 0.021 0.001 TYR D 385 ARG 0.004 0.000 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 27 time to evaluate : 0.840 Fit side-chains REVERT: D 17 ASN cc_start: 0.6435 (OUTLIER) cc_final: 0.6135 (m-40) REVERT: D 59 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7354 (mtmp) REVERT: D 96 GLN cc_start: 0.7776 (tt0) cc_final: 0.7159 (pt0) REVERT: D 162 ILE cc_start: 0.7887 (mm) cc_final: 0.7566 (mp) REVERT: D 247 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6938 (ttp80) REVERT: D 251 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: D 261 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7347 (mtpp) REVERT: D 266 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8102 (mmm-85) REVERT: D 280 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7499 (t0) REVERT: D 364 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7290 (mm-40) REVERT: D 406 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7754 (mtpt) REVERT: D 415 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8449 (p) outliers start: 26 outliers final: 10 residues processed: 47 average time/residue: 1.5870 time to fit residues: 81.5120 Evaluate side-chains 44 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 25 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 16462 Z= 0.426 Angle : 0.721 10.024 24964 Z= 0.367 Chirality : 0.041 0.295 3223 Planarity : 0.005 0.041 1096 Dihedral : 24.520 173.536 8876 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 7.29 % Allowed : 25.36 % Favored : 67.35 % 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: -0.88 (0.41), residues: 383 helix: 0.46 (0.33), residues: 236 sheet: -1.83 (0.94), residues: 24 loop : -2.34 (0.49), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 357 HIS 0.005 0.001 HIS D 109 PHE 0.012 0.002 PHE D 146 TYR 0.024 0.002 TYR D 385 ARG 0.004 0.001 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 27 time to evaluate : 0.679 Fit side-chains REVERT: D 17 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.6282 (m-40) REVERT: D 59 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7356 (mtmp) REVERT: D 201 LEU cc_start: 0.7575 (tm) cc_final: 0.7369 (tp) REVERT: D 247 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6946 (ttp80) REVERT: D 251 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: D 266 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7329 (mmm160) REVERT: D 280 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7526 (t0) REVERT: D 364 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7338 (mm-40) REVERT: D 406 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7738 (mtpt) REVERT: D 415 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8504 (p) outliers start: 25 outliers final: 12 residues processed: 48 average time/residue: 1.4208 time to fit residues: 74.6286 Evaluate side-chains 48 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 27 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16462 Z= 0.257 Angle : 0.637 9.301 24964 Z= 0.325 Chirality : 0.036 0.294 3223 Planarity : 0.004 0.044 1096 Dihedral : 24.530 174.887 8876 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 7.00 % Allowed : 25.95 % Favored : 67.06 % 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: -0.67 (0.42), residues: 383 helix: 0.62 (0.34), residues: 236 sheet: -1.66 (1.01), residues: 24 loop : -2.25 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 PHE 0.014 0.002 PHE D 89 TYR 0.019 0.002 TYR D 385 ARG 0.004 0.000 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 26 time to evaluate : 0.807 Fit side-chains REVERT: D 59 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7333 (mtmp) REVERT: D 201 LEU cc_start: 0.7611 (tm) cc_final: 0.7310 (tp) REVERT: D 247 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6961 (ttp80) REVERT: D 251 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: D 261 LYS cc_start: 0.7888 (mtmm) cc_final: 0.7342 (mtpp) REVERT: D 266 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8102 (mmm-85) REVERT: D 280 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7513 (t0) REVERT: D 364 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7330 (mm-40) REVERT: D 406 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7751 (mtpt) REVERT: D 415 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8477 (p) outliers start: 24 outliers final: 12 residues processed: 44 average time/residue: 1.4987 time to fit residues: 72.1310 Evaluate side-chains 45 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 25 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16462 Z= 0.346 Angle : 0.668 9.177 24964 Z= 0.340 Chirality : 0.038 0.293 3223 Planarity : 0.005 0.044 1096 Dihedral : 24.473 174.494 8876 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.71 % Allowed : 25.95 % Favored : 67.35 % 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: -0.74 (0.42), residues: 383 helix: 0.59 (0.34), residues: 236 sheet: -1.76 (0.97), residues: 24 loop : -2.31 (0.49), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 PHE 0.010 0.002 PHE D 146 TYR 0.023 0.002 TYR D 385 ARG 0.003 0.000 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 26 time to evaluate : 0.804 Fit side-chains REVERT: D 59 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7341 (mtmp) REVERT: D 247 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6949 (ttp80) REVERT: D 251 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: D 253 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7922 (mp) REVERT: D 261 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7362 (mtpp) REVERT: D 266 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8066 (mmm-85) REVERT: D 280 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7531 (t0) REVERT: D 364 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7267 (mm-40) REVERT: D 406 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7738 (mtpt) REVERT: D 415 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8454 (p) outliers start: 23 outliers final: 12 residues processed: 45 average time/residue: 1.5008 time to fit residues: 73.7338 Evaluate side-chains 45 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 24 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 16462 Z= 0.484 Angle : 0.759 10.348 24964 Z= 0.384 Chirality : 0.044 0.306 3223 Planarity : 0.005 0.044 1096 Dihedral : 24.522 173.781 8876 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.71 % Allowed : 26.53 % Favored : 66.76 % 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: -0.99 (0.41), residues: 383 helix: 0.39 (0.33), residues: 236 sheet: -1.90 (0.95), residues: 24 loop : -2.41 (0.48), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 357 HIS 0.004 0.001 HIS D 109 PHE 0.012 0.002 PHE D 146 TYR 0.025 0.002 TYR D 385 ARG 0.003 0.001 ARG D 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 26 time to evaluate : 0.767 Fit side-chains REVERT: D 59 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7387 (mtmp) REVERT: D 247 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6938 (ttp80) REVERT: D 251 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: D 253 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7960 (mp) REVERT: D 266 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7309 (mmm160) REVERT: D 280 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7502 (t0) REVERT: D 364 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7334 (mm-40) REVERT: D 406 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7744 (mtpt) REVERT: D 415 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8487 (p) outliers start: 23 outliers final: 12 residues processed: 44 average time/residue: 1.4331 time to fit residues: 69.0592 Evaluate side-chains 46 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 25 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 ASN D 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.181587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109599 restraints weight = 18098.548| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 0.86 r_work: 0.3047 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16462 Z= 0.163 Angle : 0.589 10.730 24964 Z= 0.298 Chirality : 0.033 0.277 3223 Planarity : 0.004 0.044 1096 Dihedral : 24.401 176.581 8876 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.37 % Allowed : 28.86 % Favored : 66.76 % 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: -0.35 (0.43), residues: 383 helix: 0.91 (0.34), residues: 236 sheet: -1.92 (0.93), residues: 24 loop : -2.11 (0.51), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 357 HIS 0.002 0.001 HIS D 109 PHE 0.012 0.002 PHE D 89 TYR 0.013 0.001 TYR D 385 ARG 0.003 0.000 ARG D 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.58 seconds wall clock time: 57 minutes 25.96 seconds (3445.96 seconds total)