Starting phenix.real_space_refine on Fri Dec 27 16:01:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdo_17616/12_2024/8pdo_17616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdo_17616/12_2024/8pdo_17616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdo_17616/12_2024/8pdo_17616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdo_17616/12_2024/8pdo_17616.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdo_17616/12_2024/8pdo_17616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdo_17616/12_2024/8pdo_17616.cif" } resolution = 3.1 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= -0.001 sd= 0.032 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 22 5.16 5 C 3564 2.51 5 N 990 2.21 5 O 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5722 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'RNA': 14} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Time building chain proxies: 5.15, per 1000 atoms: 0.90 Number of scatterers: 5722 At special positions: 0 Unit cell: (114.45, 79.8, 82.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 14 15.00 O 1132 8.00 N 990 7.00 C 3564 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: 1.47 Conformation dependent library (CDL) restraints added in 868.2 milliseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 69.1% alpha, 2.6% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.595A pdb=" N TYR A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.620A pdb=" N LEU B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 120 through 141 Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.584A pdb=" N GLN B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 151 " --> pdb=" O GLN B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 156 through 171 removed outlier: 3.854A pdb=" N LYS B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.846A pdb=" N ARG B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.789A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 256 through 268 removed outlier: 3.613A pdb=" N ARG B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 296 removed outlier: 4.860A pdb=" N LYS B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.890A pdb=" N GLY B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 344 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG A 96 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 35 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 336 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1845 1.34 - 1.46: 846 1.46 - 1.57: 3079 1.57 - 1.69: 27 1.69 - 1.81: 38 Bond restraints: 5835 Sorted by residual: bond pdb=" C VAL A 35 " pdb=" N THR A 36 " ideal model delta sigma weight residual 1.331 1.303 0.027 1.24e-02 6.50e+03 4.88e+00 bond pdb=" CB VAL B 92 " pdb=" CG1 VAL B 92 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CA GLU B 20 " pdb=" C GLU B 20 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.66e-02 3.63e+03 3.98e+00 bond pdb=" CB VAL A 92 " pdb=" CG1 VAL A 92 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.63e+00 bond pdb=" N LYS B 239 " pdb=" CA LYS B 239 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.33e-02 5.65e+03 2.83e+00 ... (remaining 5830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 7551 1.43 - 2.86: 349 2.86 - 4.29: 31 4.29 - 5.72: 3 5.72 - 7.15: 4 Bond angle restraints: 7938 Sorted by residual: angle pdb=" C LEU A 52 " pdb=" N TYR A 53 " pdb=" CA TYR A 53 " ideal model delta sigma weight residual 122.60 115.45 7.15 1.56e+00 4.11e-01 2.10e+01 angle pdb=" N ILE A 6 " pdb=" CA ILE A 6 " pdb=" C ILE A 6 " ideal model delta sigma weight residual 106.21 108.97 -2.76 1.07e+00 8.73e-01 6.66e+00 angle pdb=" C GLN A 91 " pdb=" N VAL A 92 " pdb=" CA VAL A 92 " ideal model delta sigma weight residual 120.63 123.86 -3.23 1.33e+00 5.65e-01 5.91e+00 angle pdb=" N LYS B 239 " pdb=" CA LYS B 239 " pdb=" C LYS B 239 " ideal model delta sigma weight residual 112.54 109.71 2.83 1.22e+00 6.72e-01 5.38e+00 angle pdb=" CA GLU B 20 " pdb=" C GLU B 20 " pdb=" N SER B 21 " ideal model delta sigma weight residual 117.96 120.71 -2.75 1.23e+00 6.61e-01 4.98e+00 ... (remaining 7933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3187 17.53 - 35.05: 315 35.05 - 52.58: 59 52.58 - 70.11: 13 70.11 - 87.64: 21 Dihedral angle restraints: 3595 sinusoidal: 1563 harmonic: 2032 Sorted by residual: dihedral pdb=" CA GLY B 311 " pdb=" C GLY B 311 " pdb=" N LEU B 312 " pdb=" CA LEU B 312 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LEU B 52 " pdb=" C LEU B 52 " pdb=" N TYR B 53 " pdb=" CA TYR B 53 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ALA B 251 " pdb=" C ALA B 251 " pdb=" N TYR B 252 " pdb=" CA TYR B 252 " ideal model delta harmonic sigma weight residual -180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 652 0.042 - 0.083: 226 0.083 - 0.125: 48 0.125 - 0.166: 8 0.166 - 0.208: 2 Chirality restraints: 936 Sorted by residual: chirality pdb=" CB VAL B 35 " pdb=" CA VAL B 35 " pdb=" CG1 VAL B 35 " pdb=" CG2 VAL B 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA ILE A 25 " pdb=" N ILE A 25 " pdb=" C ILE A 25 " pdb=" CB ILE A 25 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 933 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 198 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 199 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 53 " 0.007 2.00e-02 2.50e+03 1.34e-02 3.60e+00 pdb=" CG TYR A 53 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 53 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 53 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 53 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 53 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 53 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 73 " 0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 C C 73 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C C 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C C 73 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C C 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C C 73 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C C 73 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C C 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 73 " -0.005 2.00e-02 2.50e+03 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 51 2.63 - 3.20: 5295 3.20 - 3.77: 9054 3.77 - 4.33: 12859 4.33 - 4.90: 20585 Nonbonded interactions: 47844 Sorted by model distance: nonbonded pdb=" O LEU A 18 " pdb=" OG SER B 233 " model vdw 2.068 3.040 nonbonded pdb=" OG SER A 277 " pdb=" OD1 ASN A 320 " model vdw 2.138 3.040 nonbonded pdb=" O VAL A 35 " pdb=" OG1 THR A 95 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 338 " pdb=" OP2 C C 74 " model vdw 2.232 3.040 nonbonded pdb=" NH1 ARG A 27 " pdb=" O THR B 236 " model vdw 2.241 3.120 ... (remaining 47839 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' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.260 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 19.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.006 0.067 5835 Z= 0.418 Angle : 0.664 7.149 7938 Z= 0.393 Chirality : 0.044 0.208 936 Planarity : 0.004 0.051 962 Dihedral : 15.615 87.636 2291 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.19 (0.32), residues: 694 helix: 0.59 (0.24), residues: 470 sheet: -1.01 (0.87), residues: 30 loop : -0.60 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.004 0.001 HIS B 15 PHE 0.017 0.002 PHE B 224 TYR 0.031 0.003 TYR A 53 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.636 Fit side-chains REVERT: A 78 ARG cc_start: 0.7403 (mmm160) cc_final: 0.5880 (tpt-90) REVERT: A 249 MET cc_start: 0.7654 (mmt) cc_final: 0.7430 (mmt) REVERT: A 266 ARG cc_start: 0.7783 (tmt170) cc_final: 0.5836 (tpt170) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2631 time to fit residues: 27.3056 Evaluate side-chains 76 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5835 Z= 0.202 Angle : 0.483 6.157 7938 Z= 0.262 Chirality : 0.039 0.143 936 Planarity : 0.004 0.046 962 Dihedral : 11.435 74.012 987 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.50 % Allowed : 5.20 % Favored : 94.30 % 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: 0.83 (0.32), residues: 694 helix: 1.16 (0.24), residues: 474 sheet: -0.94 (0.88), residues: 30 loop : -0.61 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.003 0.001 HIS A 275 PHE 0.013 0.001 PHE B 224 TYR 0.018 0.002 TYR A 53 ARG 0.006 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.635 Fit side-chains REVERT: A 78 ARG cc_start: 0.7399 (mmm160) cc_final: 0.5828 (tpt-90) REVERT: A 266 ARG cc_start: 0.7668 (tmt170) cc_final: 0.5771 (tpt170) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.2883 time to fit residues: 27.3115 Evaluate side-chains 72 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 175 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5835 Z= 0.228 Angle : 0.477 6.126 7938 Z= 0.257 Chirality : 0.039 0.139 936 Planarity : 0.004 0.043 962 Dihedral : 11.440 74.045 987 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.34 % Allowed : 8.39 % Favored : 91.28 % 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: 0.95 (0.33), residues: 694 helix: 1.20 (0.24), residues: 478 sheet: -1.05 (0.88), residues: 30 loop : -0.40 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS B 15 PHE 0.012 0.001 PHE B 224 TYR 0.014 0.002 TYR A 53 ARG 0.006 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.640 Fit side-chains REVERT: A 78 ARG cc_start: 0.7415 (mmm160) cc_final: 0.5821 (tpt-90) REVERT: A 266 ARG cc_start: 0.7685 (tmt170) cc_final: 0.5749 (tpt170) outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 0.2655 time to fit residues: 23.1930 Evaluate side-chains 68 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 175 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 57 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5835 Z= 0.200 Angle : 0.456 6.107 7938 Z= 0.245 Chirality : 0.039 0.180 936 Planarity : 0.004 0.041 962 Dihedral : 11.431 73.954 987 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.17 % Allowed : 8.72 % Favored : 90.10 % 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: 1.06 (0.33), residues: 694 helix: 1.31 (0.24), residues: 480 sheet: -0.92 (0.88), residues: 30 loop : -0.47 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.011 0.001 PHE B 224 TYR 0.011 0.002 TYR A 59 ARG 0.007 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.671 Fit side-chains REVERT: A 78 ARG cc_start: 0.7401 (mmm160) cc_final: 0.5815 (tpt-90) REVERT: A 266 ARG cc_start: 0.7641 (tmt170) cc_final: 0.5017 (mtt180) REVERT: B 117 HIS cc_start: 0.7060 (t70) cc_final: 0.6599 (t70) REVERT: B 139 LEU cc_start: 0.8365 (tp) cc_final: 0.8005 (tt) outliers start: 7 outliers final: 3 residues processed: 77 average time/residue: 0.2751 time to fit residues: 25.7476 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5835 Z= 0.258 Angle : 0.487 6.128 7938 Z= 0.260 Chirality : 0.040 0.161 936 Planarity : 0.004 0.039 962 Dihedral : 11.448 74.191 987 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.01 % Allowed : 10.40 % Favored : 88.59 % 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: 0.93 (0.33), residues: 694 helix: 1.20 (0.24), residues: 480 sheet: -0.98 (0.89), residues: 30 loop : -0.50 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.002 0.001 HIS B 15 PHE 0.013 0.002 PHE B 224 TYR 0.015 0.002 TYR A 59 ARG 0.008 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.635 Fit side-chains REVERT: A 78 ARG cc_start: 0.7434 (mmm160) cc_final: 0.5838 (tpt-90) REVERT: A 266 ARG cc_start: 0.7691 (tmt170) cc_final: 0.5746 (tpt170) REVERT: A 284 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7393 (tm-30) outliers start: 6 outliers final: 5 residues processed: 73 average time/residue: 0.2828 time to fit residues: 25.2335 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5835 Z= 0.172 Angle : 0.442 6.048 7938 Z= 0.237 Chirality : 0.038 0.149 936 Planarity : 0.004 0.041 962 Dihedral : 11.472 73.914 987 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.84 % Allowed : 11.41 % Favored : 87.75 % 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: 1.29 (0.33), residues: 694 helix: 1.48 (0.25), residues: 476 sheet: -0.96 (0.88), residues: 30 loop : -0.28 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.003 0.001 HIS A 7 PHE 0.010 0.001 PHE B 224 TYR 0.011 0.001 TYR A 338 ARG 0.008 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.562 Fit side-chains REVERT: A 78 ARG cc_start: 0.7389 (mmm160) cc_final: 0.5783 (tpt-90) REVERT: A 266 ARG cc_start: 0.7628 (tmt170) cc_final: 0.5024 (mtt180) REVERT: B 117 HIS cc_start: 0.7116 (t70) cc_final: 0.6595 (t70) REVERT: B 139 LEU cc_start: 0.8355 (tp) cc_final: 0.7980 (tt) outliers start: 5 outliers final: 4 residues processed: 75 average time/residue: 0.2661 time to fit residues: 24.3086 Evaluate side-chains 74 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.0040 chunk 43 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5835 Z= 0.203 Angle : 0.454 6.041 7938 Z= 0.243 Chirality : 0.039 0.137 936 Planarity : 0.004 0.040 962 Dihedral : 11.480 74.029 987 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.84 % Allowed : 12.75 % Favored : 86.41 % 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: 1.28 (0.33), residues: 694 helix: 1.46 (0.25), residues: 476 sheet: -0.97 (0.89), residues: 30 loop : -0.30 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.011 0.001 PHE B 224 TYR 0.012 0.001 TYR A 59 ARG 0.009 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.626 Fit side-chains REVERT: A 78 ARG cc_start: 0.7407 (mmm160) cc_final: 0.5810 (tpt-90) REVERT: A 266 ARG cc_start: 0.7665 (tmt170) cc_final: 0.5048 (mtt180) REVERT: A 284 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 117 HIS cc_start: 0.7053 (t70) cc_final: 0.6592 (t70) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.2579 time to fit residues: 23.2212 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 0.0970 chunk 50 optimal weight: 0.1980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5835 Z= 0.129 Angle : 0.420 5.981 7938 Z= 0.224 Chirality : 0.037 0.150 936 Planarity : 0.003 0.039 962 Dihedral : 11.539 73.725 987 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.67 % Allowed : 13.09 % Favored : 86.24 % 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: 1.63 (0.33), residues: 694 helix: 1.80 (0.25), residues: 476 sheet: -1.32 (0.76), residues: 38 loop : -0.22 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 123 HIS 0.002 0.001 HIS A 7 PHE 0.008 0.001 PHE B 169 TYR 0.011 0.001 TYR A 338 ARG 0.009 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.632 Fit side-chains REVERT: A 36 THR cc_start: 0.8231 (m) cc_final: 0.8023 (m) REVERT: A 78 ARG cc_start: 0.7352 (mmm160) cc_final: 0.5727 (tpt-90) REVERT: A 266 ARG cc_start: 0.7513 (tmt170) cc_final: 0.4896 (mtt180) REVERT: B 117 HIS cc_start: 0.7023 (t70) cc_final: 0.6538 (t70) REVERT: B 139 LEU cc_start: 0.8351 (tp) cc_final: 0.8063 (tt) outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 0.2604 time to fit residues: 25.8505 Evaluate side-chains 76 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5835 Z= 0.182 Angle : 0.441 5.971 7938 Z= 0.236 Chirality : 0.038 0.155 936 Planarity : 0.004 0.040 962 Dihedral : 11.519 73.957 987 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.01 % Allowed : 13.42 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.33), residues: 694 helix: 1.76 (0.24), residues: 476 sheet: -1.33 (0.77), residues: 38 loop : -0.15 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.011 0.001 PHE B 224 TYR 0.011 0.001 TYR A 338 ARG 0.009 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.513 Fit side-chains REVERT: A 36 THR cc_start: 0.8236 (m) cc_final: 0.8017 (m) REVERT: A 78 ARG cc_start: 0.7388 (mmm160) cc_final: 0.5772 (tpt-90) REVERT: A 266 ARG cc_start: 0.7585 (tmt170) cc_final: 0.4944 (mtt180) REVERT: B 117 HIS cc_start: 0.7024 (t70) cc_final: 0.6567 (t70) REVERT: B 139 LEU cc_start: 0.8349 (tp) cc_final: 0.8071 (tt) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.2621 time to fit residues: 24.3492 Evaluate side-chains 77 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 0.0470 chunk 51 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.0870 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5835 Z= 0.133 Angle : 0.421 5.983 7938 Z= 0.226 Chirality : 0.037 0.124 936 Planarity : 0.004 0.039 962 Dihedral : 11.521 73.794 987 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.84 % Allowed : 13.76 % Favored : 85.40 % 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: 1.78 (0.33), residues: 694 helix: 1.93 (0.24), residues: 476 sheet: -1.31 (0.77), residues: 38 loop : -0.20 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.010 0.001 PHE B 224 TYR 0.011 0.001 TYR A 338 ARG 0.009 0.000 ARG B 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.634 Fit side-chains REVERT: A 36 THR cc_start: 0.8217 (m) cc_final: 0.8010 (m) REVERT: A 78 ARG cc_start: 0.7359 (mmm160) cc_final: 0.5729 (tpt-90) REVERT: A 266 ARG cc_start: 0.7488 (tmt170) cc_final: 0.4873 (mtt180) REVERT: B 117 HIS cc_start: 0.7030 (t70) cc_final: 0.6583 (t70) REVERT: B 139 LEU cc_start: 0.8314 (tp) cc_final: 0.8012 (tt) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.2477 time to fit residues: 23.4679 Evaluate side-chains 76 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 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 = 0.3855 r_free = 0.3855 target = 0.167652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146016 restraints weight = 6530.372| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.63 r_work: 0.3461 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5835 Z= 0.216 Angle : 0.465 6.004 7938 Z= 0.249 Chirality : 0.039 0.159 936 Planarity : 0.004 0.040 962 Dihedral : 11.497 73.969 987 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.84 % Allowed : 14.43 % Favored : 84.73 % 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: 1.60 (0.33), residues: 694 helix: 1.74 (0.24), residues: 476 sheet: -1.20 (0.78), residues: 38 loop : -0.14 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.003 0.001 HIS A 15 PHE 0.012 0.001 PHE B 224 TYR 0.013 0.001 TYR A 59 ARG 0.010 0.000 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.90 seconds wall clock time: 29 minutes 58.21 seconds (1798.21 seconds total)