Starting phenix.real_space_refine on Wed Jan 15 04:18:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdf_38276/01_2025/8xdf_38276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdf_38276/01_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_38276/01_2025/8xdf_38276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdf_38276/01_2025/8xdf_38276.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdf_38276/01_2025/8xdf_38276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdf_38276/01_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-5571/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: 4.98, per 1000 atoms: 0.62 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: 1.77 Conformation dependent library (CDL) restraints added in 1.0 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: 0.74 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: 2.24 Time building geometry restraints manager: 2.09 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: 0.04 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: 1.310 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: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.150 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.200 ------------------------------------------------------------------------------- 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 : 0.821 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: 0.8519 time to fit residues: 133.4058 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 : 0.736 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.089842 restraints weight = 8986.757| |-----------------------------------------------------------------------------| 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 : 0.931 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: 1.0720 time to fit residues: 124.3679 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 : 0.914 ------------------------------------------------------------------------------- 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: 0.0040 chunk 78 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 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: 3.9990 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.2396 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.110600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.088752 restraints weight = 9100.176| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.43 r_work: 0.2897 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8253 Z= 0.238 Angle : 0.555 5.921 11280 Z= 0.285 Chirality : 0.041 0.140 1323 Planarity : 0.006 0.066 1368 Dihedral : 4.347 16.666 1092 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.54 % Allowed : 12.80 % 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: 2.37 (0.26), residues: 1044 helix: 1.99 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.61 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 PHE 0.013 0.002 PHE B 301 TYR 0.015 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 124 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.848 Fit side-chains REVERT: A 366 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7996 (mmtp) REVERT: C 56 LEU cc_start: 0.7744 (mt) cc_final: 0.7518 (mp) REVERT: C 283 PHE cc_start: 0.8628 (t80) cc_final: 0.8416 (t80) REVERT: C 364 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8153 (mp) outliers start: 22 outliers final: 13 residues processed: 115 average time/residue: 1.0465 time to fit residues: 129.2307 Evaluate side-chains 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.108699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.086977 restraints weight = 9070.094| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.41 r_work: 0.2843 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8253 Z= 0.296 Angle : 0.581 6.024 11280 Z= 0.297 Chirality : 0.043 0.145 1323 Planarity : 0.006 0.067 1368 Dihedral : 4.522 17.127 1092 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.54 % Allowed : 12.57 % Favored : 84.89 % 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: 1.95 (0.18), residues: 744 sheet: None (None), residues: 0 loop : 0.49 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 171 HIS 0.005 0.001 HIS C 259 PHE 0.015 0.002 PHE A 301 TYR 0.015 0.002 TYR A 194 ARG 0.003 0.001 ARG C 114 *********************** 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 124 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.903 Fit side-chains REVERT: A 204 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8034 (pt) REVERT: A 366 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7992 (mmtp) REVERT: B 302 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8283 (mtm) REVERT: C 56 LEU cc_start: 0.7702 (mt) cc_final: 0.7478 (mp) REVERT: C 364 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8158 (mp) outliers start: 22 outliers final: 15 residues processed: 116 average time/residue: 1.0133 time to fit residues: 126.6464 Evaluate side-chains 117 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 302 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 181 ASN B 280 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.089116 restraints weight = 8977.051| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.41 r_work: 0.2882 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2064 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= 0.195 Angle : 0.531 5.870 11280 Z= 0.272 Chirality : 0.040 0.140 1323 Planarity : 0.005 0.067 1368 Dihedral : 4.297 16.590 1092 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.08 % Allowed : 12.92 % 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: 2.45 (0.26), residues: 1044 helix: 2.05 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.65 (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 C 288 TYR 0.012 0.002 TYR A 194 ARG 0.002 0.000 ARG B 114 *********************** 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 117 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.818 Fit side-chains REVERT: A 204 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.8012 (pt) REVERT: A 366 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8018 (mmtp) REVERT: C 56 LEU cc_start: 0.7697 (mt) cc_final: 0.7468 (mp) REVERT: C 364 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8152 (mp) outliers start: 18 outliers final: 13 residues processed: 112 average time/residue: 1.0068 time to fit residues: 121.4059 Evaluate side-chains 113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 364 LEU 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: 2.9990 chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.110907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.089202 restraints weight = 9034.424| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.42 r_work: 0.2873 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2106 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= 0.196 Angle : 0.532 5.856 11280 Z= 0.272 Chirality : 0.040 0.139 1323 Planarity : 0.005 0.067 1368 Dihedral : 4.273 16.338 1092 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.19 % Allowed : 13.03 % 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: 2.52 (0.26), residues: 1044 helix: 2.13 (0.18), residues: 744 sheet: None (None), residues: 0 loop : 0.62 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 369 ARG 0.002 0.000 ARG B 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 116 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.875 Fit side-chains REVERT: A 204 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8009 (pt) REVERT: A 366 LYS cc_start: 0.8262 (mmtt) cc_final: 0.8026 (mmtp) REVERT: B 256 MET cc_start: 0.8820 (mtp) cc_final: 0.8486 (mtp) REVERT: C 56 LEU cc_start: 0.7748 (mt) cc_final: 0.7516 (mp) REVERT: C 213 SER cc_start: 0.7932 (t) cc_final: 0.7698 (m) REVERT: C 364 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8180 (mp) outliers start: 19 outliers final: 14 residues processed: 112 average time/residue: 1.0225 time to fit residues: 123.2819 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 : 0.827 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.111202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.089523 restraints weight = 9066.710| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.42 r_work: 0.2885 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2121 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 : 0.522 5.843 11280 Z= 0.267 Chirality : 0.040 0.138 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.231 16.050 1092 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.19 % Allowed : 12.69 % Favored : 85.12 % 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: 2.53 (0.26), residues: 1044 helix: 2.09 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.74 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 PHE 0.012 0.001 PHE C 288 TYR 0.011 0.002 TYR A 369 ARG 0.002 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 120 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.941 Fit side-chains REVERT: A 204 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8005 (pt) REVERT: A 366 LYS cc_start: 0.8266 (mmtt) cc_final: 0.8034 (mmtp) REVERT: B 256 MET cc_start: 0.8794 (mtp) cc_final: 0.8445 (mtp) REVERT: C 56 LEU cc_start: 0.7732 (mt) cc_final: 0.7497 (mp) REVERT: C 213 SER cc_start: 0.7921 (t) cc_final: 0.7698 (m) REVERT: C 364 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8171 (mp) outliers start: 19 outliers final: 14 residues processed: 116 average time/residue: 1.0329 time to fit residues: 128.9574 Evaluate side-chains 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3224 r_free = 0.3224 target = 0.109062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.087265 restraints weight = 9132.803| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.42 r_work: 0.2846 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8253 Z= 0.274 Angle : 0.573 6.010 11280 Z= 0.292 Chirality : 0.043 0.145 1323 Planarity : 0.006 0.067 1368 Dihedral : 4.487 16.709 1092 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.08 % Allowed : 12.80 % Favored : 85.12 % 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: 2.31 (0.26), residues: 1044 helix: 1.91 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.72 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 171 HIS 0.005 0.001 HIS C 259 PHE 0.014 0.002 PHE A 301 TYR 0.013 0.002 TYR B 369 ARG 0.002 0.000 ARG B 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 113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.949 Fit side-chains REVERT: A 204 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8036 (pt) REVERT: A 366 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8059 (mmtp) REVERT: C 56 LEU cc_start: 0.7693 (mt) cc_final: 0.7468 (mp) REVERT: C 364 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8189 (mp) outliers start: 18 outliers final: 15 residues processed: 109 average time/residue: 1.0018 time to fit residues: 117.7046 Evaluate side-chains 111 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 70 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3258 r_free = 0.3258 target = 0.111645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.089926 restraints weight = 9252.606| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.44 r_work: 0.2906 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2169 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= 0.181 Angle : 0.520 5.810 11280 Z= 0.266 Chirality : 0.040 0.138 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.246 15.817 1092 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.73 % Allowed : 13.38 % Favored : 84.89 % 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: 2.52 (0.26), residues: 1044 helix: 2.07 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.75 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 171 HIS 0.004 0.001 HIS A 259 PHE 0.012 0.001 PHE C 288 TYR 0.011 0.002 TYR B 369 ARG 0.002 0.000 ARG C 114 *********************** 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 110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.899 Fit side-chains REVERT: A 204 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.8018 (pt) REVERT: A 366 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7828 (mmtp) REVERT: C 56 LEU cc_start: 0.7736 (mt) cc_final: 0.7499 (mp) REVERT: C 213 SER cc_start: 0.7936 (t) cc_final: 0.7698 (m) REVERT: C 364 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8140 (mp) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.9684 time to fit residues: 110.7543 Evaluate side-chains 108 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 204 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.0570 chunk 26 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.112662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.091104 restraints weight = 9009.418| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.41 r_work: 0.2904 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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= 0.170 Angle : 0.515 5.803 11280 Z= 0.262 Chirality : 0.040 0.137 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.188 15.479 1092 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.61 % Allowed : 13.84 % 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: 2.58 (0.26), residues: 1044 helix: 2.06 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.94 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 171 HIS 0.003 0.001 HIS A 259 PHE 0.012 0.001 PHE C 288 TYR 0.011 0.002 TYR C 369 ARG 0.002 0.000 ARG B 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 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.932 Fit side-chains REVERT: A 204 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8023 (pt) REVERT: A 366 LYS cc_start: 0.8298 (mmtt) cc_final: 0.8072 (mmtp) REVERT: C 56 LEU cc_start: 0.7734 (mt) cc_final: 0.7493 (mp) REVERT: C 213 SER cc_start: 0.7947 (t) cc_final: 0.7720 (m) outliers start: 14 outliers final: 11 residues processed: 110 average time/residue: 1.0388 time to fit residues: 122.8078 Evaluate side-chains 109 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 308 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3269 r_free = 0.3269 target = 0.112294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.090642 restraints weight = 9104.680| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.44 r_work: 0.2904 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2204 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 : 0.516 5.816 11280 Z= 0.262 Chirality : 0.040 0.137 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.167 15.360 1092 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.61 % Allowed : 13.73 % 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: 2.62 (0.26), residues: 1044 helix: 2.09 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.95 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 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 C 369 ARG 0.002 0.000 ARG B 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5050.65 seconds wall clock time: 90 minutes 15.91 seconds (5415.91 seconds total)