Starting phenix.real_space_refine on Wed Mar 12 13:58:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdf_38276/03_2025/8xdf_38276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdf_38276/03_2025/8xdf_38276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xdf_38276/03_2025/8xdf_38276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdf_38276/03_2025/8xdf_38276.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdf_38276/03_2025/8xdf_38276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdf_38276/03_2025/8xdf_38276.cif" } resolution = 2.4 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= 0.002 sd= 0.041 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 69 5.16 5 C 5331 2.51 5 N 1239 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8025 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 330} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 330} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 330} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.09, per 1000 atoms: 0.76 Number of scatterers: 8025 At special positions: 0 Unit cell: (100.04, 94.3, 73.8, 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 69 16.00 O 1386 8.00 N 1239 7.00 C 5331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.93 Conformation dependent library (CDL) restraints added in 1.2 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 74 through 89 Processing helix chain 'A' and resid 89 through 110 Processing helix chain 'A' and resid 113 through 119 Processing helix chain 'A' and resid 123 through 136 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 169 removed outlier: 3.852A pdb=" N THR A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.691A pdb=" N LEU A 217 " --> pdb=" O TRP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.854A pdb=" N ILE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.623A pdb=" N SER A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 274 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.501A pdb=" N ILE A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 305 through 332 removed outlier: 3.684A pdb=" N GLU A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 74 through 89 Processing helix chain 'B' and resid 89 through 110 Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 123 through 136 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 169 removed outlier: 3.852A pdb=" N THR B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 213 through 217 removed outlier: 3.691A pdb=" N LEU B 217 " --> pdb=" O TRP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.855A pdb=" N ILE B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 238 through 253 removed outlier: 3.623A pdb=" N SER B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 274 Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 305 through 332 removed outlier: 3.683A pdb=" N GLU B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'C' and resid 34 through 38 Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 74 through 89 Processing helix chain 'C' and resid 89 through 110 Processing helix chain 'C' and resid 113 through 119 Processing helix chain 'C' and resid 123 through 136 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 169 removed outlier: 3.852A pdb=" N THR C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS C 157 " --> pdb=" O MET C 153 " (cutoff:3.500A) Proline residue: C 158 - end of helix Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.691A pdb=" N LEU C 217 " --> pdb=" O TRP C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.855A pdb=" N ILE C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 253 removed outlier: 3.623A pdb=" N SER C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 274 Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'C' and resid 288 through 298 Processing helix chain 'C' and resid 305 through 332 removed outlier: 3.682A pdb=" N GLU C 332 " --> pdb=" O ASN C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 Processing helix chain 'C' and resid 369 through 383 540 hydrogen bonds defined for protein. 1593 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: 2.41 Time building geometry restraints manager: 2.29 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: 1427 1.33 - 1.45: 2109 1.45 - 1.57: 4603 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 8253 Sorted by residual: bond pdb=" CA ILE A 281 " pdb=" C ILE A 281 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.22e-02 6.72e+03 1.70e+01 bond pdb=" N GLU A 279 " pdb=" CA GLU A 279 " ideal model delta sigma weight residual 1.459 1.422 0.037 1.23e-02 6.61e+03 8.94e+00 bond pdb=" CA GLY A 284 " pdb=" C GLY A 284 " ideal model delta sigma weight residual 1.511 1.473 0.039 1.37e-02 5.33e+03 7.92e+00 bond pdb=" C GLY A 287 " pdb=" N PHE A 288 " ideal model delta sigma weight residual 1.332 1.295 0.036 1.35e-02 5.49e+03 7.27e+00 bond pdb=" N LEU A 285 " pdb=" CA LEU A 285 " ideal model delta sigma weight residual 1.458 1.423 0.035 1.33e-02 5.65e+03 6.86e+00 ... (remaining 8248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11108 2.00 - 3.99: 144 3.99 - 5.99: 26 5.99 - 7.99: 1 7.99 - 9.99: 1 Bond angle restraints: 11280 Sorted by residual: angle pdb=" N PHE A 283 " pdb=" CA PHE A 283 " pdb=" CB PHE A 283 " ideal model delta sigma weight residual 110.44 103.52 6.92 1.53e+00 4.27e-01 2.05e+01 angle pdb=" N GLY A 287 " pdb=" CA GLY A 287 " pdb=" C GLY A 287 " ideal model delta sigma weight residual 113.18 123.17 -9.99 2.37e+00 1.78e-01 1.78e+01 angle pdb=" N ASN A 280 " pdb=" CA ASN A 280 " pdb=" C ASN A 280 " ideal model delta sigma weight residual 111.36 115.20 -3.84 1.09e+00 8.42e-01 1.24e+01 angle pdb=" N THR C 177 " pdb=" CA THR C 177 " pdb=" C THR C 177 " ideal model delta sigma weight residual 113.19 108.07 5.12 1.58e+00 4.01e-01 1.05e+01 angle pdb=" N THR B 177 " pdb=" CA THR B 177 " pdb=" C THR B 177 " ideal model delta sigma weight residual 113.19 108.09 5.10 1.58e+00 4.01e-01 1.04e+01 ... (remaining 11275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 3908 11.91 - 23.82: 523 23.82 - 35.73: 220 35.73 - 47.64: 68 47.64 - 59.55: 36 Dihedral angle restraints: 4755 sinusoidal: 1746 harmonic: 3009 Sorted by residual: dihedral pdb=" N PHE A 283 " pdb=" C PHE A 283 " pdb=" CA PHE A 283 " pdb=" CB PHE A 283 " ideal model delta harmonic sigma weight residual 122.80 113.57 9.23 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" CA LEU C 304 " pdb=" C LEU C 304 " pdb=" N THR C 305 " pdb=" CA THR C 305 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA LEU A 304 " pdb=" C LEU A 304 " pdb=" N THR A 305 " pdb=" CA THR A 305 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 4752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1229 0.081 - 0.162: 90 0.162 - 0.243: 2 0.243 - 0.324: 1 0.324 - 0.405: 1 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA ASN A 280 " pdb=" N ASN A 280 " pdb=" C ASN A 280 " pdb=" CB ASN A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA LEU A 285 " pdb=" N LEU A 285 " pdb=" C LEU A 285 " pdb=" CB LEU A 285 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA TRP A 286 " pdb=" N TRP A 286 " pdb=" C TRP A 286 " pdb=" CB TRP A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1320 not shown) Planarity restraints: 1368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 283 " 0.028 2.00e-02 2.50e+03 2.02e-02 7.11e+00 pdb=" CG PHE A 283 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 283 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 283 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 283 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 283 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 283 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 281 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C ILE A 281 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE A 281 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR A 282 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 369 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 370 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.033 5.00e-02 4.00e+02 ... (remaining 1365 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1943 2.79 - 3.32: 8069 3.32 - 3.84: 14269 3.84 - 4.37: 17284 4.37 - 4.90: 28366 Nonbonded interactions: 69931 Sorted by model distance: nonbonded pdb=" O GLY C 263 " pdb=" OG SER C 290 " model vdw 2.262 3.040 nonbonded pdb=" O GLY B 263 " pdb=" OG SER B 290 " model vdw 2.263 3.040 nonbonded pdb=" O GLY A 263 " pdb=" OG SER A 290 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR A 100 " pdb=" OG1 THR A 127 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR C 100 " pdb=" OG1 THR C 127 " model vdw 2.291 3.040 ... (remaining 69926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 8253 Z= 0.306 Angle : 0.566 9.987 11280 Z= 0.315 Chirality : 0.044 0.405 1323 Planarity : 0.006 0.059 1368 Dihedral : 14.784 59.549 2829 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 15.80 % Favored : 84.20 % 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 (0.26), residues: 1044 helix: 1.60 (0.19), residues: 735 sheet: None (None), residues: 0 loop : 0.43 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 306 HIS 0.004 0.001 HIS A 259 PHE 0.042 0.002 PHE A 283 TYR 0.017 0.002 TYR C 194 ARG 0.001 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.818 Fit side-chains REVERT: B 167 VAL cc_start: 0.8053 (t) cc_final: 0.7680 (t) REVERT: C 56 LEU cc_start: 0.7869 (mt) cc_final: 0.7669 (mp) REVERT: C 352 MET cc_start: 0.8675 (ttp) cc_final: 0.8475 (ttp) REVERT: C 362 MET cc_start: 0.8457 (mmm) cc_final: 0.8206 (mmm) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.8228 time to fit residues: 128.8062 Evaluate side-chains 110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 280 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.089842 restraints weight = 8986.759| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.42 r_work: 0.2915 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8253 Z= 0.238 Angle : 0.569 5.937 11280 Z= 0.294 Chirality : 0.041 0.137 1323 Planarity : 0.006 0.067 1368 Dihedral : 4.325 16.079 1092 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.73 % Allowed : 13.73 % Favored : 84.54 % 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: 2.27 (0.26), residues: 1044 helix: 1.92 (0.19), residues: 747 sheet: None (None), residues: 0 loop : 0.58 (0.40), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 PHE 0.014 0.002 PHE A 301 TYR 0.015 0.002 TYR A 194 ARG 0.001 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.821 Fit side-chains REVERT: A 366 LYS cc_start: 0.8233 (mmtt) cc_final: 0.8015 (mmtp) REVERT: C 56 LEU cc_start: 0.7699 (mt) cc_final: 0.7463 (mt) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 1.0854 time to fit residues: 125.6547 Evaluate side-chains 108 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.089882 restraints weight = 9101.276| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.43 r_work: 0.2916 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8253 Z= 0.204 Angle : 0.534 5.868 11280 Z= 0.274 Chirality : 0.040 0.137 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.237 16.291 1092 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.31 % Allowed : 13.26 % Favored : 84.43 % 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: 2.46 (0.26), residues: 1044 helix: 2.06 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.64 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 PHE 0.012 0.001 PHE A 301 TYR 0.014 0.002 TYR A 194 ARG 0.002 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.842 Fit side-chains REVERT: A 366 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7992 (mmtp) REVERT: B 237 ASP cc_start: 0.8921 (p0) cc_final: 0.8718 (p0) REVERT: C 56 LEU cc_start: 0.7739 (mt) cc_final: 0.7507 (mp) REVERT: C 364 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8169 (mp) outliers start: 20 outliers final: 11 residues processed: 115 average time/residue: 1.0099 time to fit residues: 124.8154 Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.090007 restraints weight = 9052.954| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.43 r_work: 0.2893 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8253 Z= 0.187 Angle : 0.520 5.855 11280 Z= 0.266 Chirality : 0.040 0.135 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.181 16.047 1092 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.19 % Allowed : 13.26 % Favored : 84.54 % 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: 2.54 (0.26), residues: 1044 helix: 2.13 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.66 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 PHE 0.012 0.001 PHE A 301 TYR 0.012 0.002 TYR A 194 ARG 0.001 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.927 Fit side-chains REVERT: A 204 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7989 (pt) REVERT: A 366 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7989 (mmtp) REVERT: C 56 LEU cc_start: 0.7727 (mt) cc_final: 0.7506 (mp) REVERT: C 283 PHE cc_start: 0.8626 (t80) cc_final: 0.8421 (t80) REVERT: C 364 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8167 (mp) outliers start: 19 outliers final: 15 residues processed: 113 average time/residue: 0.9877 time to fit residues: 120.3459 Evaluate side-chains 118 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 87 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.090390 restraints weight = 8988.428| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.42 r_work: 0.2899 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8253 Z= 0.179 Angle : 0.520 5.834 11280 Z= 0.266 Chirality : 0.040 0.136 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.154 15.794 1092 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.31 % Allowed : 13.26 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.26), residues: 1044 helix: 2.18 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.68 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 171 HIS 0.003 0.001 HIS A 259 PHE 0.011 0.001 PHE A 301 TYR 0.011 0.002 TYR C 369 ARG 0.001 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.939 Fit side-chains REVERT: A 204 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7980 (pt) REVERT: A 366 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7979 (mmtp) REVERT: B 256 MET cc_start: 0.8724 (mtp) cc_final: 0.8347 (mtp) REVERT: C 56 LEU cc_start: 0.7709 (mt) cc_final: 0.7490 (mp) REVERT: C 283 PHE cc_start: 0.8564 (t80) cc_final: 0.8161 (t80) REVERT: C 364 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8170 (mp) outliers start: 20 outliers final: 14 residues processed: 115 average time/residue: 1.0646 time to fit residues: 131.7211 Evaluate side-chains 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 92 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.090394 restraints weight = 9035.361| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.42 r_work: 0.2901 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8253 Z= 0.176 Angle : 0.512 5.823 11280 Z= 0.261 Chirality : 0.040 0.136 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.139 15.670 1092 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.31 % Allowed : 13.26 % Favored : 84.43 % 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: 2.65 (0.26), residues: 1044 helix: 2.16 (0.18), residues: 753 sheet: None (None), residues: 0 loop : 0.81 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 171 HIS 0.003 0.001 HIS A 259 PHE 0.011 0.001 PHE B 301 TYR 0.011 0.002 TYR C 369 ARG 0.001 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.814 Fit side-chains REVERT: A 366 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7854 (mmtp) REVERT: C 56 LEU cc_start: 0.7705 (mt) cc_final: 0.7488 (mp) REVERT: C 213 SER cc_start: 0.7913 (t) cc_final: 0.7685 (m) REVERT: C 283 PHE cc_start: 0.8564 (t80) cc_final: 0.8168 (t80) REVERT: C 364 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8176 (mp) outliers start: 20 outliers final: 14 residues processed: 120 average time/residue: 0.9228 time to fit residues: 119.6175 Evaluate side-chains 118 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.090148 restraints weight = 9068.815| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.42 r_work: 0.2889 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8253 Z= 0.185 Angle : 0.517 5.841 11280 Z= 0.264 Chirality : 0.040 0.136 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.177 15.733 1092 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.96 % Allowed : 13.38 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.26), residues: 1044 helix: 2.13 (0.18), residues: 753 sheet: None (None), residues: 0 loop : 0.80 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 171 HIS 0.003 0.001 HIS A 259 PHE 0.012 0.001 PHE A 301 TYR 0.011 0.002 TYR C 369 ARG 0.001 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.820 Fit side-chains REVERT: A 204 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8001 (pt) REVERT: A 366 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7867 (mmtp) REVERT: B 256 MET cc_start: 0.8743 (mtp) cc_final: 0.8406 (mtp) REVERT: C 56 LEU cc_start: 0.7730 (mt) cc_final: 0.7498 (mp) REVERT: C 213 SER cc_start: 0.7927 (t) cc_final: 0.7702 (m) REVERT: C 283 PHE cc_start: 0.8573 (t80) cc_final: 0.8178 (t80) REVERT: C 364 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8182 (mp) outliers start: 17 outliers final: 14 residues processed: 117 average time/residue: 1.0082 time to fit residues: 126.8284 Evaluate side-chains 119 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 0.0270 chunk 79 optimal weight: 3.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.088870 restraints weight = 9132.147| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.43 r_work: 0.2873 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8253 Z= 0.214 Angle : 0.537 5.910 11280 Z= 0.273 Chirality : 0.041 0.140 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.300 16.253 1092 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.19 % Allowed : 12.80 % Favored : 85.01 % 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: 2.50 (0.26), residues: 1044 helix: 2.08 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.70 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 PHE 0.013 0.001 PHE A 301 TYR 0.012 0.002 TYR C 369 ARG 0.001 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.831 Fit side-chains REVERT: A 204 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8022 (pt) REVERT: A 366 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7825 (mmtp) REVERT: B 256 MET cc_start: 0.8774 (mtp) cc_final: 0.8379 (mtp) REVERT: C 56 LEU cc_start: 0.7744 (mt) cc_final: 0.7517 (mp) REVERT: C 283 PHE cc_start: 0.8564 (t80) cc_final: 0.8163 (t80) REVERT: C 364 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8183 (mp) outliers start: 19 outliers final: 14 residues processed: 113 average time/residue: 0.9561 time to fit residues: 116.4280 Evaluate side-chains 113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 103 optimal weight: 0.0020 chunk 70 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.091021 restraints weight = 9255.175| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.45 r_work: 0.2911 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8253 Z= 0.165 Angle : 0.510 5.781 11280 Z= 0.260 Chirality : 0.039 0.136 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.133 15.469 1092 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.61 % Allowed : 13.61 % Favored : 84.78 % 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: 2.63 (0.26), residues: 1044 helix: 2.13 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.86 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 171 HIS 0.003 0.001 HIS A 259 PHE 0.012 0.001 PHE C 288 TYR 0.011 0.001 TYR A 369 ARG 0.001 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.900 Fit side-chains REVERT: A 204 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7974 (pt) REVERT: A 366 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7704 (mmtp) REVERT: B 256 MET cc_start: 0.8700 (mtp) cc_final: 0.8366 (mtp) REVERT: C 56 LEU cc_start: 0.7697 (mt) cc_final: 0.7467 (mp) REVERT: C 213 SER cc_start: 0.7904 (t) cc_final: 0.7676 (m) REVERT: C 283 PHE cc_start: 0.8516 (t80) cc_final: 0.8115 (t80) outliers start: 14 outliers final: 8 residues processed: 117 average time/residue: 0.9873 time to fit residues: 124.1604 Evaluate side-chains 111 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 308 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 0.0370 chunk 76 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.091296 restraints weight = 8995.324| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.41 r_work: 0.2918 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8253 Z= 0.167 Angle : 0.514 5.798 11280 Z= 0.262 Chirality : 0.040 0.135 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.133 15.315 1092 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.38 % Allowed : 14.19 % Favored : 84.43 % 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: 2.63 (0.26), residues: 1044 helix: 2.11 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.90 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 171 HIS 0.003 0.001 HIS A 259 PHE 0.012 0.001 PHE C 288 TYR 0.011 0.001 TYR B 369 ARG 0.001 0.000 ARG A 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.887 Fit side-chains REVERT: A 204 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7985 (pt) REVERT: A 366 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7732 (mmtp) REVERT: C 56 LEU cc_start: 0.7706 (mt) cc_final: 0.7475 (mp) REVERT: C 213 SER cc_start: 0.7924 (t) cc_final: 0.7694 (m) REVERT: C 283 PHE cc_start: 0.8530 (t80) cc_final: 0.8214 (t80) REVERT: C 364 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8172 (mp) outliers start: 12 outliers final: 10 residues processed: 116 average time/residue: 0.9465 time to fit residues: 118.3352 Evaluate side-chains 117 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 0.0070 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.091121 restraints weight = 9100.870| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.42 r_work: 0.2927 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8253 Z= 0.173 Angle : 0.519 5.814 11280 Z= 0.264 Chirality : 0.040 0.139 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.149 15.242 1092 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.38 % Allowed : 14.19 % Favored : 84.43 % 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: 2.68 (0.26), residues: 1044 helix: 2.11 (0.18), residues: 753 sheet: None (None), residues: 0 loop : 1.07 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 171 HIS 0.004 0.001 HIS A 259 PHE 0.012 0.001 PHE A 301 TYR 0.011 0.002 TYR A 369 ARG 0.001 0.000 ARG A 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5581.88 seconds wall clock time: 95 minutes 59.51 seconds (5759.51 seconds total)