Starting phenix.real_space_refine on Sat May 10 09:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdo_17616/05_2025/8pdo_17616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdo_17616/05_2025/8pdo_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_17616/05_2025/8pdo_17616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdo_17616/05_2025/8pdo_17616.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdo_17616/05_2025/8pdo_17616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdo_17616/05_2025/8pdo_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-5687/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: 5.12, per 1000 atoms: 0.89 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: 1.52 Conformation dependent library (CDL) restraints added in 809.0 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: 1.95 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: 1.80 Time building geometry restraints manager: 1.76 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 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: 0.050 Process input model: 20.200 Find NCS groups from input model: 0.160 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- 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= 0.278 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 Details of bonding type rmsd hydrogen bonds : bond 0.12984 ( 336) hydrogen bonds : angle 5.84367 ( 987) covalent geometry : bond 0.00648 ( 5835) covalent geometry : angle 0.66374 ( 7938) *********************** 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 : 0.586 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: 0.2550 time to fit residues: 26.3507 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 : 0.583 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.159989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139003 restraints weight = 6596.059| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.58 r_work: 0.3431 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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= 0.140 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 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 336) hydrogen bonds : angle 4.43646 ( 987) covalent geometry : bond 0.00315 ( 5835) covalent geometry : angle 0.48324 ( 7938) *********************** 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 : 0.600 Fit side-chains REVERT: A 78 ARG cc_start: 0.7382 (mmm160) cc_final: 0.5356 (tpt-90) REVERT: A 266 ARG cc_start: 0.7746 (tmt170) cc_final: 0.5589 (tpt170) REVERT: A 337 MET cc_start: 0.8668 (tpp) cc_final: 0.8386 (mmp) REVERT: B 129 LYS cc_start: 0.7276 (pttm) cc_final: 0.7058 (pptt) REVERT: B 196 LYS cc_start: 0.7799 (mttt) cc_final: 0.7518 (ttpp) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.2913 time to fit residues: 27.4371 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 : 0.665 ------------------------------------------------------------------------------- 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 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.154139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.132027 restraints weight = 6650.110| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.64 r_work: 0.3368 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5835 Z= 0.209 Angle : 0.527 6.311 7938 Z= 0.283 Chirality : 0.042 0.140 936 Planarity : 0.004 0.044 962 Dihedral : 11.447 74.306 987 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.67 % Allowed : 8.39 % Favored : 90.94 % 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: 0.75 (0.32), residues: 694 helix: 1.06 (0.24), residues: 474 sheet: -1.10 (0.89), residues: 30 loop : -0.49 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 123 HIS 0.003 0.001 HIS B 15 PHE 0.014 0.002 PHE B 224 TYR 0.017 0.002 TYR A 59 ARG 0.006 0.001 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.05034 ( 336) hydrogen bonds : angle 4.43714 ( 987) covalent geometry : bond 0.00498 ( 5835) covalent geometry : angle 0.52713 ( 7938) *********************** 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 76 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.972 Fit side-chains REVERT: A 78 ARG cc_start: 0.7422 (mmm160) cc_final: 0.5346 (tpt-90) REVERT: A 266 ARG cc_start: 0.7836 (tmt170) cc_final: 0.5608 (tpt170) REVERT: B 196 LYS cc_start: 0.7748 (mttt) cc_final: 0.7493 (ttpp) outliers start: 4 outliers final: 4 residues processed: 74 average time/residue: 0.3164 time to fit residues: 28.6239 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 : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 92 VAL 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 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.0570 chunk 28 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.156483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135030 restraints weight = 6718.637| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.62 r_work: 0.3392 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5835 Z= 0.156 Angle : 0.476 6.121 7938 Z= 0.256 Chirality : 0.040 0.143 936 Planarity : 0.004 0.041 962 Dihedral : 11.435 74.034 987 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.84 % Allowed : 9.73 % Favored : 89.43 % 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: 0.90 (0.33), residues: 694 helix: 1.16 (0.24), residues: 478 sheet: -1.12 (0.87), residues: 30 loop : -0.36 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.003 0.001 HIS A 7 PHE 0.012 0.001 PHE B 224 TYR 0.013 0.002 TYR A 59 ARG 0.008 0.001 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 336) hydrogen bonds : angle 4.25061 ( 987) covalent geometry : bond 0.00363 ( 5835) covalent geometry : angle 0.47595 ( 7938) *********************** 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 78 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.668 Fit side-chains REVERT: A 78 ARG cc_start: 0.7434 (mmm160) cc_final: 0.5379 (tpt-90) REVERT: A 135 MET cc_start: 0.6998 (ttt) cc_final: 0.6754 (ttt) REVERT: A 266 ARG cc_start: 0.7751 (tmt170) cc_final: 0.4735 (mtt180) REVERT: B 196 LYS cc_start: 0.7697 (mttt) cc_final: 0.7433 (ttpp) outliers start: 5 outliers final: 2 residues processed: 75 average time/residue: 0.3212 time to fit residues: 28.8747 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 : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.153913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.132342 restraints weight = 6630.717| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.62 r_work: 0.3389 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5835 Z= 0.166 Angle : 0.483 6.129 7938 Z= 0.259 Chirality : 0.040 0.208 936 Planarity : 0.004 0.040 962 Dihedral : 11.436 74.112 987 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.01 % Allowed : 11.24 % 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: 0.84 (0.33), residues: 694 helix: 1.14 (0.24), residues: 480 sheet: -1.09 (0.88), residues: 30 loop : -0.53 (0.46), 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 0.012 0.001 PHE B 224 TYR 0.014 0.002 TYR A 59 ARG 0.008 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 336) hydrogen bonds : angle 4.23811 ( 987) covalent geometry : bond 0.00390 ( 5835) covalent geometry : angle 0.48338 ( 7938) *********************** 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 79 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.605 Fit side-chains REVERT: A 78 ARG cc_start: 0.7413 (mmm160) cc_final: 0.5359 (tpt-90) REVERT: A 135 MET cc_start: 0.7025 (ttt) cc_final: 0.6790 (ttt) REVERT: A 266 ARG cc_start: 0.7759 (tmt170) cc_final: 0.4742 (mtt180) REVERT: A 284 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7241 (tm-30) REVERT: B 129 LYS cc_start: 0.7339 (pttm) cc_final: 0.7133 (pptt) REVERT: B 196 LYS cc_start: 0.7694 (mttt) cc_final: 0.7430 (ttpp) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 0.2857 time to fit residues: 26.7395 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 : 0.620 ------------------------------------------------------------------------------- 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 188 ASN Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.152111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.129607 restraints weight = 6690.696| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.68 r_work: 0.3382 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5835 Z= 0.163 Angle : 0.479 6.118 7938 Z= 0.257 Chirality : 0.040 0.174 936 Planarity : 0.004 0.040 962 Dihedral : 11.428 74.074 987 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.17 % Allowed : 12.08 % Favored : 86.74 % 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: 0.87 (0.33), residues: 694 helix: 1.18 (0.24), residues: 480 sheet: -1.13 (0.87), residues: 30 loop : -0.55 (0.46), 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 0.012 0.001 PHE B 224 TYR 0.013 0.002 TYR A 59 ARG 0.009 0.001 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 336) hydrogen bonds : angle 4.20646 ( 987) covalent geometry : bond 0.00385 ( 5835) covalent geometry : angle 0.47851 ( 7938) *********************** 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 79 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.641 Fit side-chains REVERT: A 78 ARG cc_start: 0.7414 (mmm160) cc_final: 0.5369 (tpt-90) REVERT: A 135 MET cc_start: 0.7002 (ttt) cc_final: 0.6754 (ttt) REVERT: A 266 ARG cc_start: 0.7765 (tmt170) cc_final: 0.4624 (mtt180) REVERT: B 129 LYS cc_start: 0.7361 (pttm) cc_final: 0.7160 (pptt) REVERT: B 196 LYS cc_start: 0.7680 (mttt) cc_final: 0.7438 (ttpp) REVERT: B 282 LEU cc_start: 0.8674 (mt) cc_final: 0.8412 (mt) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.2619 time to fit residues: 24.2918 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 : 0.666 ------------------------------------------------------------------------------- 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 188 ASN Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 66 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 overall best weight: 0.3336 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.170176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.151342 restraints weight = 6501.203| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.37 r_work: 0.3274 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5835 Z= 0.110 Angle : 0.436 6.023 7938 Z= 0.235 Chirality : 0.038 0.153 936 Planarity : 0.004 0.040 962 Dihedral : 11.467 73.834 987 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.84 % Allowed : 13.42 % Favored : 85.74 % 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: 1.47 (0.25), residues: 476 sheet: -1.06 (0.87), 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 0.010 0.001 PHE B 224 TYR 0.012 0.001 TYR A 338 ARG 0.009 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 336) hydrogen bonds : angle 4.02235 ( 987) covalent geometry : bond 0.00240 ( 5835) covalent geometry : angle 0.43609 ( 7938) *********************** 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 80 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.575 Fit side-chains REVERT: A 36 THR cc_start: 0.8275 (m) cc_final: 0.8057 (m) REVERT: A 78 ARG cc_start: 0.7433 (mmm160) cc_final: 0.5440 (tpt-90) REVERT: A 135 MET cc_start: 0.6958 (ttt) cc_final: 0.6648 (ttt) REVERT: A 266 ARG cc_start: 0.7694 (tmt170) cc_final: 0.4758 (mtt180) REVERT: B 117 HIS cc_start: 0.7168 (t70) cc_final: 0.6638 (t70) REVERT: B 139 LEU cc_start: 0.8262 (tp) cc_final: 0.8003 (tt) REVERT: B 196 LYS cc_start: 0.7707 (mttt) cc_final: 0.7460 (ttpp) outliers start: 5 outliers final: 1 residues processed: 77 average time/residue: 0.2723 time to fit residues: 25.3556 Evaluate side-chains 72 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.0020 chunk 0 optimal weight: 1.9990 overall best weight: 0.4506 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.169245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.150642 restraints weight = 6454.162| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.31 r_work: 0.3496 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5835 Z= 0.126 Angle : 0.445 6.023 7938 Z= 0.239 Chirality : 0.039 0.136 936 Planarity : 0.004 0.039 962 Dihedral : 11.460 73.981 987 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.67 % Allowed : 13.26 % Favored : 86.07 % 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: 1.32 (0.33), residues: 694 helix: 1.51 (0.24), residues: 476 sheet: -1.06 (0.88), residues: 30 loop : -0.32 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.010 0.001 PHE B 224 TYR 0.012 0.001 TYR A 338 ARG 0.009 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 336) hydrogen bonds : angle 4.01091 ( 987) covalent geometry : bond 0.00287 ( 5835) covalent geometry : angle 0.44482 ( 7938) *********************** 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 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.583 Fit side-chains REVERT: A 78 ARG cc_start: 0.7579 (mmm160) cc_final: 0.5688 (tpt-90) REVERT: A 135 MET cc_start: 0.6987 (ttt) cc_final: 0.6758 (ttt) REVERT: A 201 MET cc_start: 0.8375 (ttp) cc_final: 0.8126 (ttm) REVERT: A 266 ARG cc_start: 0.7779 (tmt170) cc_final: 0.4902 (mtt180) REVERT: A 284 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7402 (tm-30) REVERT: B 117 HIS cc_start: 0.7254 (t70) cc_final: 0.6683 (t70) REVERT: B 139 LEU cc_start: 0.8292 (tp) cc_final: 0.8023 (tt) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.2712 time to fit residues: 24.3349 Evaluate side-chains 70 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.159870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.138304 restraints weight = 6596.065| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.57 r_work: 0.3427 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5835 Z= 0.177 Angle : 0.490 6.116 7938 Z= 0.262 Chirality : 0.041 0.162 936 Planarity : 0.004 0.039 962 Dihedral : 11.441 74.122 987 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.50 % Allowed : 13.93 % 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: 1.00 (0.32), residues: 694 helix: 1.29 (0.24), residues: 480 sheet: -1.14 (0.86), residues: 30 loop : -0.54 (0.46), residues: 184 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 0.013 0.002 PHE B 224 TYR 0.015 0.002 TYR A 59 ARG 0.010 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 336) hydrogen bonds : angle 4.16475 ( 987) covalent geometry : bond 0.00419 ( 5835) covalent geometry : angle 0.49037 ( 7938) *********************** 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 71 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.583 Fit side-chains REVERT: A 78 ARG cc_start: 0.7458 (mmm160) cc_final: 0.5428 (tpt-90) REVERT: A 135 MET cc_start: 0.6936 (ttt) cc_final: 0.6647 (ttt) REVERT: A 266 ARG cc_start: 0.7732 (tmt170) cc_final: 0.4646 (mtt180) REVERT: A 284 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7286 (tm-30) REVERT: B 282 LEU cc_start: 0.8672 (mt) cc_final: 0.8409 (mt) outliers start: 3 outliers final: 2 residues processed: 70 average time/residue: 0.2681 time to fit residues: 22.9479 Evaluate side-chains 70 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.157232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135906 restraints weight = 6826.544| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.54 r_work: 0.3407 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5835 Z= 0.139 Angle : 0.458 6.086 7938 Z= 0.246 Chirality : 0.039 0.147 936 Planarity : 0.004 0.041 962 Dihedral : 11.453 74.010 987 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.50 % Allowed : 13.93 % 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: 1.13 (0.33), residues: 694 helix: 1.42 (0.24), residues: 480 sheet: -1.15 (0.85), residues: 30 loop : -0.58 (0.46), residues: 184 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 338 ARG 0.010 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 336) hydrogen bonds : angle 4.07597 ( 987) covalent geometry : bond 0.00321 ( 5835) covalent geometry : angle 0.45838 ( 7938) ********************** 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 71 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.687 Fit side-chains REVERT: A 78 ARG cc_start: 0.7474 (mmm160) cc_final: 0.5472 (tpt-90) REVERT: A 135 MET cc_start: 0.6967 (ttt) cc_final: 0.6698 (ttt) REVERT: A 266 ARG cc_start: 0.7843 (tmt170) cc_final: 0.4765 (mtt180) REVERT: A 284 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 282 LEU cc_start: 0.8688 (mt) cc_final: 0.8448 (mt) REVERT: B 346 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7058 (tm-30) outliers start: 3 outliers final: 2 residues processed: 71 average time/residue: 0.2665 time to fit residues: 23.2153 Evaluate side-chains 70 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 346 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.0030 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.162073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.140620 restraints weight = 6739.642| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.60 r_work: 0.3462 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5835 Z= 0.130 Angle : 0.451 6.069 7938 Z= 0.242 Chirality : 0.039 0.144 936 Planarity : 0.004 0.042 962 Dihedral : 11.459 73.960 987 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: 1.34 (0.33), residues: 694 helix: 1.55 (0.24), residues: 476 sheet: -1.12 (0.86), residues: 30 loop : -0.37 (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 338 ARG 0.010 0.000 ARG B 208 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 336) hydrogen bonds : angle 4.02993 ( 987) covalent geometry : bond 0.00298 ( 5835) covalent geometry : angle 0.45114 ( 7938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.69 seconds wall clock time: 58 minutes 2.53 seconds (3482.53 seconds total)