Starting phenix.real_space_refine on Wed Nov 13 23:27:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggl_40012/11_2024/8ggl_40012.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggl_40012/11_2024/8ggl_40012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggl_40012/11_2024/8ggl_40012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggl_40012/11_2024/8ggl_40012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggl_40012/11_2024/8ggl_40012.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggl_40012/11_2024/8ggl_40012.cif" } resolution = 3.2 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= -0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 1436 2.51 5 N 340 2.21 5 O 359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2151 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2135 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.73, per 1000 atoms: 1.27 Number of scatterers: 2151 At special positions: 0 Unit cell: (56.4005, 82.4315, 61.6067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 359 8.00 N 340 7.00 C 1436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 279.7 milliseconds 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 544 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 87.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 33 through 61 removed outlier: 3.754A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 97 removed outlier: 4.252A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.736A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 148 through 171 removed outlier: 4.142A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.637A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.936A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 287 Processing helix chain 'R' and resid 288 through 299 removed outlier: 3.661A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 315 removed outlier: 3.549A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 320 Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 341 161 hydrogen bonds defined for protein. 477 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: 0.56 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 362 1.33 - 1.45: 606 1.45 - 1.57: 1215 1.57 - 1.69: 0 1.69 - 1.82: 22 Bond restraints: 2205 Sorted by residual: bond pdb=" C MET R 36 " pdb=" N GLY R 37 " ideal model delta sigma weight residual 1.334 1.298 0.036 1.21e-02 6.83e+03 8.61e+00 bond pdb=" CA MET R 36 " pdb=" C MET R 36 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.39e-02 5.18e+03 8.32e+00 bond pdb=" CA MET R 36 " pdb=" CB MET R 36 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.68e-02 3.54e+03 6.88e+00 bond pdb=" CA VAL R 33 " pdb=" CB VAL R 33 " ideal model delta sigma weight residual 1.540 1.505 0.036 1.36e-02 5.41e+03 6.83e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.27e+00 ... (remaining 2200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 2960 1.69 - 3.39: 45 3.39 - 5.08: 12 5.08 - 6.78: 4 6.78 - 8.47: 1 Bond angle restraints: 3022 Sorted by residual: angle pdb=" N GLY R 35 " pdb=" CA GLY R 35 " pdb=" C GLY R 35 " ideal model delta sigma weight residual 112.73 121.20 -8.47 1.20e+00 6.94e-01 4.99e+01 angle pdb=" C VAL R 34 " pdb=" CA VAL R 34 " pdb=" CB VAL R 34 " ideal model delta sigma weight residual 112.14 105.60 6.54 1.35e+00 5.49e-01 2.35e+01 angle pdb=" CA GLY R 35 " pdb=" C GLY R 35 " pdb=" O GLY R 35 " ideal model delta sigma weight residual 120.75 116.78 3.97 1.03e+00 9.43e-01 1.49e+01 angle pdb=" CA GLY R 35 " pdb=" C GLY R 35 " pdb=" N MET R 36 " ideal model delta sigma weight residual 117.04 120.67 -3.63 9.90e-01 1.02e+00 1.34e+01 angle pdb=" N MET R 36 " pdb=" CA MET R 36 " pdb=" C MET R 36 " ideal model delta sigma weight residual 112.89 108.92 3.97 1.24e+00 6.50e-01 1.02e+01 ... (remaining 3017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.10: 1079 11.10 - 22.21: 116 22.21 - 33.31: 45 33.31 - 44.41: 15 44.41 - 55.52: 5 Dihedral angle restraints: 1260 sinusoidal: 424 harmonic: 836 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB MET R 171 " pdb=" CG MET R 171 " pdb=" SD MET R 171 " pdb=" CE MET R 171 " ideal model delta sinusoidal sigma weight residual 180.00 127.53 52.47 3 1.50e+01 4.44e-03 9.12e+00 dihedral pdb=" CG ARG R 328 " pdb=" CD ARG R 328 " pdb=" NE ARG R 328 " pdb=" CZ ARG R 328 " ideal model delta sinusoidal sigma weight residual 180.00 -140.45 -39.55 2 1.50e+01 4.44e-03 8.65e+00 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 219 0.029 - 0.059: 97 0.059 - 0.088: 38 0.088 - 0.117: 19 0.117 - 0.146: 1 Chirality restraints: 374 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VAL R 33 " pdb=" N VAL R 33 " pdb=" C VAL R 33 " pdb=" CB VAL R 33 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA VAL R 34 " pdb=" N VAL R 34 " pdb=" C VAL R 34 " pdb=" CB VAL R 34 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.09e-01 ... (remaining 371 not shown) Planarity restraints: 360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP R 32 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C TRP R 32 " 0.058 2.00e-02 2.50e+03 pdb=" O TRP R 32 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL R 33 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 34 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C VAL R 34 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL R 34 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY R 35 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO R 211 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.024 5.00e-02 4.00e+02 ... (remaining 357 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 652 2.83 - 3.35: 2124 3.35 - 3.86: 3356 3.86 - 4.38: 3610 4.38 - 4.90: 6603 Nonbonded interactions: 16345 Sorted by model distance: nonbonded pdb=" O SER R 111 " pdb=" OG SER R 165 " model vdw 2.312 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.323 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAK G1I R 501 " model vdw 2.482 3.040 nonbonded pdb=" O ARG R 175 " pdb=" ND2 ASN R 196 " model vdw 2.589 3.120 nonbonded pdb=" N MET R 36 " pdb=" N GLY R 37 " model vdw 2.602 2.560 ... (remaining 16340 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.510 Find NCS groups from input model: 0.020 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.005 0.050 2205 Z= 0.335 Angle : 0.618 8.473 3022 Z= 0.371 Chirality : 0.041 0.146 374 Planarity : 0.004 0.042 360 Dihedral : 12.383 55.517 713 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 1.05 (0.50), residues: 278 helix: 1.49 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.07 (0.64), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 217 TYR 0.008 0.001 TYR R 199 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.254 Fit side-chains REVERT: R 161 SER cc_start: 0.8768 (m) cc_final: 0.8466 (m) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2512 time to fit residues: 6.6173 Evaluate side-chains 20 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2205 Z= 0.256 Angle : 0.506 5.430 3022 Z= 0.281 Chirality : 0.039 0.105 374 Planarity : 0.004 0.046 360 Dihedral : 4.455 18.489 313 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.82 % Allowed : 5.16 % Favored : 92.02 % 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: 1.19 (0.49), residues: 278 helix: 1.58 (0.35), residues: 215 sheet: None (None), residues: 0 loop : -2.02 (0.63), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 158 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 217 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.254 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 24 average time/residue: 0.2248 time to fit residues: 6.2390 Evaluate side-chains 24 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8293 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2205 Z= 0.217 Angle : 0.473 5.334 3022 Z= 0.262 Chirality : 0.039 0.103 374 Planarity : 0.003 0.043 360 Dihedral : 4.343 18.562 313 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.76 % Allowed : 6.10 % Favored : 90.14 % 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 (0.49), residues: 278 helix: 1.83 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -1.95 (0.60), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 158 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 217 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.354 Fit side-chains REVERT: R 296 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8539 (p-80) outliers start: 8 outliers final: 7 residues processed: 25 average time/residue: 0.2454 time to fit residues: 7.0485 Evaluate side-chains 26 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8328 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2205 Z= 0.269 Angle : 0.501 5.433 3022 Z= 0.277 Chirality : 0.040 0.108 374 Planarity : 0.004 0.043 360 Dihedral : 4.454 18.961 313 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 4.23 % Allowed : 8.45 % Favored : 87.32 % 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: 1.49 (0.49), residues: 278 helix: 1.89 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -1.65 (0.61), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 217 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.244 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 26 average time/residue: 0.2167 time to fit residues: 6.4854 Evaluate side-chains 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2205 Z= 0.180 Angle : 0.445 5.257 3022 Z= 0.246 Chirality : 0.038 0.105 374 Planarity : 0.003 0.036 360 Dihedral : 4.171 18.395 313 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.76 % Allowed : 10.80 % Favored : 85.45 % 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: 1.86 (0.50), residues: 278 helix: 2.19 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.62 (0.61), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 217 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.241 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 26 average time/residue: 0.1978 time to fit residues: 6.0171 Evaluate side-chains 26 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.8278 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2205 Z= 0.188 Angle : 0.448 5.303 3022 Z= 0.247 Chirality : 0.039 0.176 374 Planarity : 0.003 0.035 360 Dihedral : 4.161 18.420 313 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.23 % Allowed : 11.27 % Favored : 84.51 % 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: 1.95 (0.50), residues: 278 helix: 2.25 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.57 (0.63), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.007 0.001 PHE R 61 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.252 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 27 average time/residue: 0.2104 time to fit residues: 6.6573 Evaluate side-chains 26 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8305 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2205 Z= 0.224 Angle : 0.474 5.362 3022 Z= 0.261 Chirality : 0.039 0.144 374 Planarity : 0.003 0.035 360 Dihedral : 4.276 18.884 313 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.76 % Allowed : 11.74 % Favored : 84.51 % 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: 1.82 (0.49), residues: 278 helix: 2.19 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -1.70 (0.62), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.007 0.001 PHE R 61 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.205 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 25 average time/residue: 0.1912 time to fit residues: 5.6096 Evaluate side-chains 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.8248 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2205 Z= 0.156 Angle : 0.432 5.264 3022 Z= 0.238 Chirality : 0.038 0.126 374 Planarity : 0.003 0.033 360 Dihedral : 4.027 18.228 313 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.76 % Allowed : 11.74 % Favored : 84.51 % 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: 2.12 (0.50), residues: 278 helix: 2.36 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -1.53 (0.63), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.002 0.001 HIS R 178 PHE 0.007 0.001 PHE R 217 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.240 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 28 average time/residue: 0.1901 time to fit residues: 6.2117 Evaluate side-chains 29 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 22 optimal weight: 0.0070 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2205 Z= 0.128 Angle : 0.406 5.214 3022 Z= 0.223 Chirality : 0.037 0.121 374 Planarity : 0.003 0.027 360 Dihedral : 3.803 17.573 313 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.35 % Allowed : 13.62 % Favored : 84.04 % 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: 2.41 (0.51), residues: 278 helix: 2.64 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.58 (0.63), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.002 0.001 HIS R 178 PHE 0.007 0.001 PHE R 61 TYR 0.005 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.244 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.2071 time to fit residues: 6.4535 Evaluate side-chains 25 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8282 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2205 Z= 0.203 Angle : 0.458 5.335 3022 Z= 0.251 Chirality : 0.039 0.116 374 Planarity : 0.003 0.028 360 Dihedral : 4.130 18.322 313 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.35 % Allowed : 14.08 % Favored : 83.57 % 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: 2.21 (0.50), residues: 278 helix: 2.34 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -1.43 (0.67), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.007 0.001 PHE R 217 TYR 0.008 0.001 TYR R 199 ARG 0.000 0.000 ARG R 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.253 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 25 average time/residue: 0.2238 time to fit residues: 6.5288 Evaluate side-chains 25 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 22 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.102842 restraints weight = 2793.214| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.48 r_work: 0.2998 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2205 Z= 0.161 Angle : 0.431 5.262 3022 Z= 0.236 Chirality : 0.038 0.114 374 Planarity : 0.003 0.026 360 Dihedral : 3.988 17.959 313 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.29 % Allowed : 13.15 % Favored : 83.57 % 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: 2.29 (0.50), residues: 278 helix: 2.52 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.53 (0.64), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.002 0.001 HIS R 178 PHE 0.007 0.001 PHE R 217 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 987.83 seconds wall clock time: 18 minutes 32.41 seconds (1112.41 seconds total)