Starting phenix.real_space_refine on Sat Dec 28 06:33:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdf_38276/12_2024/8xdf_38276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdf_38276/12_2024/8xdf_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_38276/12_2024/8xdf_38276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdf_38276/12_2024/8xdf_38276.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdf_38276/12_2024/8xdf_38276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdf_38276/12_2024/8xdf_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-5532/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: 4.68, per 1000 atoms: 0.58 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: 1.98 Conformation dependent library (CDL) restraints added in 1.1 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: 0.80 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: 2.15 Time building geometry restraints manager: 2.28 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.140 Find NCS groups from input model: 0.200 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- 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 : 0.909 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: 0.8765 time to fit residues: 136.7795 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 : 0.887 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 : 0.915 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 1.0798 time to fit residues: 125.1576 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 : 0.945 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.0170 chunk 29 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 76 optimal weight: 0.8980 overall best weight: 0.5736 ------------------------------------------------------------------------------- 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 ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1760 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= 0.163 Angle : 0.507 5.789 11280 Z= 0.260 Chirality : 0.039 0.135 1323 Planarity : 0.005 0.070 1368 Dihedral : 4.082 15.643 1092 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.38 % Allowed : 14.42 % 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: 2.57 (0.26), residues: 1044 helix: 2.12 (0.18), residues: 753 sheet: None (None), residues: 0 loop : 0.75 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 171 HIS 0.003 0.001 HIS A 259 PHE 0.010 0.001 PHE A 301 TYR 0.012 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 116 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.817 Fit side-chains REVERT: A 204 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8169 (pt) REVERT: B 56 LEU cc_start: 0.7916 (mt) cc_final: 0.7665 (mp) REVERT: C 364 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8254 (mp) outliers start: 12 outliers final: 3 residues processed: 112 average time/residue: 1.0037 time to fit residues: 121.3191 Evaluate side-chains 105 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 94 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 0.0010 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 181 ASN C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2038 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= 0.305 Angle : 0.598 6.034 11280 Z= 0.307 Chirality : 0.043 0.142 1323 Planarity : 0.006 0.069 1368 Dihedral : 4.522 17.036 1092 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.65 % Allowed : 12.92 % 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: 2.26 (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 0.002 HIS C 259 PHE 0.015 0.002 PHE A 301 TYR 0.014 0.002 TYR A 194 ARG 0.001 0.000 ARG C 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 122 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.909 Fit side-chains REVERT: B 302 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8279 (mtm) REVERT: C 364 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8283 (mp) outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 1.0358 time to fit residues: 125.8552 Evaluate side-chains 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 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 84 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2029 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= 0.201 Angle : 0.531 5.887 11280 Z= 0.272 Chirality : 0.040 0.139 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.302 16.704 1092 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.96 % Allowed : 13.61 % 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: 2.43 (0.26), residues: 1044 helix: 2.03 (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 0.018 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 PHE 0.012 0.001 PHE B 301 TYR 0.012 0.002 TYR A 194 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 115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.915 Fit side-chains REVERT: C 364 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8291 (mp) outliers start: 17 outliers final: 14 residues processed: 111 average time/residue: 1.0688 time to fit residues: 127.3236 Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8253 Z= 0.221 Angle : 0.544 5.923 11280 Z= 0.279 Chirality : 0.041 0.140 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.350 16.635 1092 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.08 % Allowed : 13.15 % 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: 2.41 (0.26), residues: 1044 helix: 2.01 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.68 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 171 HIS 0.004 0.001 HIS A 259 PHE 0.013 0.001 PHE B 301 TYR 0.012 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 114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.821 Fit side-chains REVERT: A 204 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8227 (pt) REVERT: C 364 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8298 (mp) outliers start: 18 outliers final: 14 residues processed: 109 average time/residue: 1.0308 time to fit residues: 120.6849 Evaluate side-chains 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2112 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= 0.189 Angle : 0.522 5.847 11280 Z= 0.267 Chirality : 0.040 0.138 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.250 16.292 1092 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: 2.49 (0.26), residues: 1044 helix: 2.07 (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 0.023 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 C 369 ARG 0.001 0.000 ARG A 64 *********************** 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 117 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.907 Fit side-chains REVERT: A 204 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8211 (pt) REVERT: B 256 MET cc_start: 0.8678 (mtp) cc_final: 0.8407 (mtp) REVERT: C 364 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8275 (mp) outliers start: 18 outliers final: 14 residues processed: 113 average time/residue: 1.0111 time to fit residues: 123.1528 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 : 0.903 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8253 Z= 0.245 Angle : 0.556 5.958 11280 Z= 0.283 Chirality : 0.042 0.141 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.409 16.567 1092 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.12 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: 2.36 (0.26), residues: 1044 helix: 1.95 (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 0.026 0.001 TRP A 171 HIS 0.005 0.001 HIS A 259 PHE 0.014 0.001 PHE A 301 TYR 0.012 0.002 TYR A 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 113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.889 Fit side-chains REVERT: B 256 MET cc_start: 0.8718 (mtp) cc_final: 0.8416 (mtp) REVERT: C 364 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8302 (mp) outliers start: 22 outliers final: 16 residues processed: 110 average time/residue: 0.9647 time to fit residues: 114.6918 Evaluate side-chains 108 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2159 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 : 0.519 5.819 11280 Z= 0.265 Chirality : 0.040 0.141 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.241 16.081 1092 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.96 % Allowed : 12.69 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.26), residues: 1044 helix: 2.06 (0.18), residues: 753 sheet: None (None), residues: 0 loop : 0.78 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 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 B 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 112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.830 Fit side-chains REVERT: A 204 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8211 (pt) REVERT: C 364 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8271 (mp) outliers start: 17 outliers final: 13 residues processed: 108 average time/residue: 0.9829 time to fit residues: 114.6058 Evaluate side-chains 107 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 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 99 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8253 Z= 0.374 Angle : 0.629 6.150 11280 Z= 0.322 Chirality : 0.046 0.151 1323 Planarity : 0.006 0.067 1368 Dihedral : 4.671 16.747 1092 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.85 % Allowed : 13.38 % 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: 2.21 (0.26), residues: 1044 helix: 1.81 (0.18), residues: 741 sheet: None (None), residues: 0 loop : 0.80 (0.40), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 171 HIS 0.007 0.002 HIS C 259 PHE 0.016 0.002 PHE B 301 TYR 0.015 0.002 TYR A 187 ARG 0.002 0.000 ARG C 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 113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.921 Fit side-chains REVERT: A 204 ILE cc_start: 0.8500 (pt) cc_final: 0.8285 (pt) REVERT: C 364 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8311 (mp) outliers start: 16 outliers final: 15 residues processed: 109 average time/residue: 1.0661 time to fit residues: 124.8623 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 : 0.844 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.111384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.089758 restraints weight = 9005.207| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.41 r_work: 0.2911 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2208 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= 0.180 Angle : 0.527 5.814 11280 Z= 0.271 Chirality : 0.040 0.142 1323 Planarity : 0.005 0.066 1368 Dihedral : 4.321 16.324 1092 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.38 % Allowed : 13.61 % 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: 2.47 (0.26), residues: 1044 helix: 1.97 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.94 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 171 HIS 0.003 0.001 HIS A 259 PHE 0.012 0.001 PHE C 288 TYR 0.012 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: 2673.64 seconds wall clock time: 49 minutes 7.21 seconds (2947.21 seconds total)