Starting phenix.real_space_refine on Sat Apr 26 15:54:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggl_40012/04_2025/8ggl_40012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggl_40012/04_2025/8ggl_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/cci-nas-00/data/ceres_data/8ggl_40012/04_2025/8ggl_40012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggl_40012/04_2025/8ggl_40012.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggl_40012/04_2025/8ggl_40012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggl_40012/04_2025/8ggl_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-5669/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: 2.35, per 1000 atoms: 1.09 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: 0.60 Conformation dependent library (CDL) restraints added in 287.3 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: 0.25 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: 0.53 Time building geometry restraints manager: 0.72 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.260 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.430 ------------------------------------------------------------------------------- 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 2206 Z= 0.266 Angle : 0.619 8.473 3024 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 Details of bonding type rmsd hydrogen bonds : bond 0.15324 ( 161) hydrogen bonds : angle 5.46665 ( 477) SS BOND : bond 0.00001 ( 1) SS BOND : angle 1.30885 ( 2) covalent geometry : bond 0.00494 ( 2205) covalent geometry : angle 0.61794 ( 3022) *********************** 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 : 0.227 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: 0.2384 time to fit residues: 6.2662 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 : 0.224 ------------------------------------------------------------------------------- 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: 0.5980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.100619 restraints weight = 2864.124| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.52 r_work: 0.2972 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2206 Z= 0.157 Angle : 0.492 5.397 3024 Z= 0.272 Chirality : 0.039 0.103 374 Planarity : 0.004 0.045 360 Dihedral : 4.386 18.285 313 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.35 % Allowed : 5.16 % Favored : 92.49 % 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: 1.27 (0.50), residues: 278 helix: 1.64 (0.35), residues: 215 sheet: None (None), residues: 0 loop : -2.01 (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 199 ARG 0.001 0.000 ARG R 328 Details of bonding type rmsd hydrogen bonds : bond 0.06839 ( 161) hydrogen bonds : angle 4.28170 ( 477) SS BOND : bond 0.00091 ( 1) SS BOND : angle 1.09913 ( 2) covalent geometry : bond 0.00357 ( 2205) covalent geometry : angle 0.49154 ( 3022) *********************** 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 24 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.226 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 24 average time/residue: 0.2136 time to fit residues: 5.9155 Evaluate side-chains 23 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.111787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.097877 restraints weight = 2868.958| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.50 r_work: 0.2926 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2206 Z= 0.182 Angle : 0.511 5.442 3024 Z= 0.283 Chirality : 0.040 0.108 374 Planarity : 0.004 0.045 360 Dihedral : 4.508 18.887 313 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.23 % Allowed : 7.51 % Favored : 88.26 % 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: 1.21 (0.49), residues: 278 helix: 1.66 (0.35), 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 0.009 0.001 PHE R 332 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 131 Details of bonding type rmsd hydrogen bonds : bond 0.07456 ( 161) hydrogen bonds : angle 4.26100 ( 477) SS BOND : bond 0.00122 ( 1) SS BOND : angle 1.21770 ( 2) covalent geometry : bond 0.00433 ( 2205) covalent geometry : angle 0.51015 ( 3022) *********************** 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 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.248 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 25 average time/residue: 0.2277 time to fit residues: 6.5864 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 : 0.246 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.113750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099782 restraints weight = 2789.071| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.49 r_work: 0.2961 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2206 Z= 0.146 Angle : 0.467 5.321 3024 Z= 0.258 Chirality : 0.038 0.103 374 Planarity : 0.003 0.041 360 Dihedral : 4.306 18.681 313 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 3.29 % Allowed : 9.39 % 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: 1.65 (0.49), residues: 278 helix: 2.02 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.64 (0.60), 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 Details of bonding type rmsd hydrogen bonds : bond 0.06584 ( 161) hydrogen bonds : angle 4.10144 ( 477) SS BOND : bond 0.00140 ( 1) SS BOND : angle 1.12051 ( 2) covalent geometry : bond 0.00326 ( 2205) covalent geometry : angle 0.46605 ( 3022) *********************** 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 27 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.250 Fit side-chains REVERT: R 148 ASN cc_start: 0.8801 (t0) cc_final: 0.8575 (t0) outliers start: 7 outliers final: 7 residues processed: 26 average time/residue: 0.2219 time to fit residues: 6.6570 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 : 0.240 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 25 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.099807 restraints weight = 2873.742| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.51 r_work: 0.2952 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2206 Z= 0.148 Angle : 0.467 5.347 3024 Z= 0.257 Chirality : 0.039 0.105 374 Planarity : 0.003 0.038 360 Dihedral : 4.287 18.820 313 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.23 % Allowed : 10.80 % Favored : 84.98 % 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: 1.73 (0.49), residues: 278 helix: 2.08 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.63 (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 328 Details of bonding type rmsd hydrogen bonds : bond 0.06607 ( 161) hydrogen bonds : angle 4.07103 ( 477) SS BOND : bond 0.00134 ( 1) SS BOND : angle 1.06320 ( 2) covalent geometry : bond 0.00331 ( 2205) covalent geometry : angle 0.46609 ( 3022) *********************** 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: 9 poor density : 18 time to evaluate : 0.241 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 26 average time/residue: 0.1881 time to fit residues: 5.7767 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 : 0.212 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 5 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.115996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.101941 restraints weight = 2811.890| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.49 r_work: 0.2983 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2206 Z= 0.123 Angle : 0.438 5.257 3024 Z= 0.241 Chirality : 0.038 0.174 374 Planarity : 0.003 0.035 360 Dihedral : 4.119 18.235 313 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 1.97 (0.50), residues: 278 helix: 2.29 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.62 (0.62), 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 217 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 Details of bonding type rmsd hydrogen bonds : bond 0.05825 ( 161) hydrogen bonds : angle 3.96324 ( 477) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.97375 ( 2) covalent geometry : bond 0.00259 ( 2205) covalent geometry : angle 0.43736 ( 3022) *********************** 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 30 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.251 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 28 average time/residue: 0.1974 time to fit residues: 6.4737 Evaluate side-chains 28 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.113951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100045 restraints weight = 2856.590| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.50 r_work: 0.2953 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2206 Z= 0.148 Angle : 0.470 5.361 3024 Z= 0.258 Chirality : 0.039 0.143 374 Planarity : 0.003 0.035 360 Dihedral : 4.255 18.833 313 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.76 % Allowed : 11.27 % Favored : 84.98 % 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: 1.89 (0.50), residues: 278 helix: 2.24 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -1.64 (0.63), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 PHE 0.007 0.001 PHE R 217 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 Details of bonding type rmsd hydrogen bonds : bond 0.06535 ( 161) hydrogen bonds : angle 4.03602 ( 477) SS BOND : bond 0.00150 ( 1) SS BOND : angle 0.99242 ( 2) covalent geometry : bond 0.00339 ( 2205) covalent geometry : angle 0.46976 ( 3022) *********************** 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 28 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.249 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 26 average time/residue: 0.1941 time to fit residues: 5.9154 Evaluate side-chains 28 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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: 0.7980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 13 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.115035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100965 restraints weight = 2909.966| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.52 r_work: 0.2981 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2206 Z= 0.130 Angle : 0.449 5.287 3024 Z= 0.247 Chirality : 0.038 0.127 374 Planarity : 0.003 0.034 360 Dihedral : 4.131 18.580 313 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 2.04 (0.50), residues: 278 helix: 2.31 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.52 (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 217 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 Details of bonding type rmsd hydrogen bonds : bond 0.06021 ( 161) hydrogen bonds : angle 3.96945 ( 477) SS BOND : bond 0.00135 ( 1) SS BOND : angle 0.96764 ( 2) covalent geometry : bond 0.00284 ( 2205) covalent geometry : angle 0.44856 ( 3022) *********************** 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 : 0.238 Fit side-chains revert: symmetry clash REVERT: R 161 SER cc_start: 0.8662 (m) cc_final: 0.8460 (m) outliers start: 8 outliers final: 8 residues processed: 28 average time/residue: 0.1925 time to fit residues: 6.3147 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 : 0.235 ------------------------------------------------------------------------------- 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 7 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 0.0470 chunk 4 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target = 0.114252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.100285 restraints weight = 2830.181| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.49 r_work: 0.2968 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2206 Z= 0.136 Angle : 0.455 5.321 3024 Z= 0.250 Chirality : 0.038 0.119 374 Planarity : 0.003 0.033 360 Dihedral : 4.155 18.701 313 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.76 % Allowed : 12.21 % 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: 2.00 (0.50), residues: 278 helix: 2.32 (0.36), residues: 203 sheet: None (None), residues: 0 loop : -1.61 (0.63), 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 Details of bonding type rmsd hydrogen bonds : bond 0.06193 ( 161) hydrogen bonds : angle 3.97727 ( 477) SS BOND : bond 0.00148 ( 1) SS BOND : angle 0.96225 ( 2) covalent geometry : bond 0.00303 ( 2205) covalent geometry : angle 0.45458 ( 3022) *********************** 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 30 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: R 161 SER cc_start: 0.8651 (m) cc_final: 0.8448 (m) outliers start: 8 outliers final: 8 residues processed: 28 average time/residue: 0.1806 time to fit residues: 5.9115 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 : 0.219 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.115142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101230 restraints weight = 2810.465| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.48 r_work: 0.2970 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2206 Z= 0.135 Angle : 0.454 5.314 3024 Z= 0.249 Chirality : 0.038 0.115 374 Planarity : 0.003 0.030 360 Dihedral : 4.144 18.657 313 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.76 % Allowed : 12.21 % 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: 2.04 (0.50), residues: 278 helix: 2.36 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -1.60 (0.63), 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 Details of bonding type rmsd hydrogen bonds : bond 0.06146 ( 161) hydrogen bonds : angle 3.96497 ( 477) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.95581 ( 2) covalent geometry : bond 0.00298 ( 2205) covalent geometry : angle 0.45328 ( 3022) ********************** 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 30 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: R 161 SER cc_start: 0.8660 (m) cc_final: 0.8456 (m) outliers start: 8 outliers final: 8 residues processed: 28 average time/residue: 0.1882 time to fit residues: 6.2849 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 : 0.228 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3212 r_free = 0.3212 target = 0.113746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099763 restraints weight = 2840.110| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.49 r_work: 0.2954 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2206 Z= 0.146 Angle : 0.466 5.350 3024 Z= 0.256 Chirality : 0.039 0.114 374 Planarity : 0.003 0.029 360 Dihedral : 4.215 18.725 313 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.76 % Allowed : 12.21 % 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: 1.97 (0.50), residues: 278 helix: 2.15 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.46 (0.66), residues: 69 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 Details of bonding type rmsd hydrogen bonds : bond 0.06463 ( 161) hydrogen bonds : angle 4.01040 ( 477) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.96833 ( 2) covalent geometry : bond 0.00330 ( 2205) covalent geometry : angle 0.46566 ( 3022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1574.08 seconds wall clock time: 27 minutes 46.45 seconds (1666.45 seconds total)