Starting phenix.real_space_refine on Wed Aug 5 05:45:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8blo_16110/08_2026/8blo_16110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8blo_16110/08_2026/8blo_16110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8blo_16110/08_2026/8blo_16110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8blo_16110/08_2026/8blo_16110.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8blo_16110/08_2026/8blo_16110.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8blo_16110/08_2026/8blo_16110.cif" model { file = "/net/cci-nas-00/data/ceres_data/8blo_16110/08_2026/8blo_16110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8blo_16110/08_2026/8blo_16110.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.152 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 3 5.49 5 S 51 5.16 5 C 5724 2.51 5 N 1239 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8487 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2646 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 19, 'TRANS': 332} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Unusual residues: {'LMN': 5, 'PLD': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'PLD:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Restraints were copied for chains: C, B Time building chain proxies: 1.67, per 1000 atoms: 0.20 Number of scatterers: 8487 At special positions: 0 Unit cell: (97.58, 103.32, 72.98, 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 51 16.00 P 3 15.00 O 1470 8.00 N 1239 7.00 C 5724 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: 1.02 Conformation dependent library (CDL) restraints added in 369.6 milliseconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 75.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 removed outlier: 3.579A pdb=" N TYR A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 134 through 149 Processing helix chain 'A' and resid 149 through 170 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 215 through 229 removed outlier: 4.474A pdb=" N VAL A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 251 Processing helix chain 'A' and resid 278 through 292 removed outlier: 4.003A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 298 through 313 Processing helix chain 'A' and resid 313 through 334 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.811A pdb=" N LEU A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 391 Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.966A pdb=" N VAL A 427 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'C' and resid 93 through 98 removed outlier: 3.579A pdb=" N TYR C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 113 through 128 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 134 through 149 Processing helix chain 'C' and resid 149 through 170 Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 215 through 229 removed outlier: 4.474A pdb=" N VAL C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 251 Processing helix chain 'C' and resid 278 through 292 removed outlier: 4.003A pdb=" N ILE C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Proline residue: C 287 - end of helix Processing helix chain 'C' and resid 298 through 313 Processing helix chain 'C' and resid 313 through 334 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 347 through 358 removed outlier: 3.809A pdb=" N LEU C 352 " --> pdb=" O TYR C 348 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 391 Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 423 through 427 removed outlier: 3.967A pdb=" N VAL C 427 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.579A pdb=" N TYR B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 113 through 128 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 134 through 149 Processing helix chain 'B' and resid 149 through 170 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 215 through 229 removed outlier: 4.474A pdb=" N VAL B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 251 Processing helix chain 'B' and resid 278 through 292 removed outlier: 4.003A pdb=" N ILE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Proline residue: B 287 - end of helix Processing helix chain 'B' and resid 298 through 313 Processing helix chain 'B' and resid 313 through 334 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 347 through 358 removed outlier: 3.809A pdb=" N LEU B 352 " --> pdb=" O TYR B 348 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 391 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.967A pdb=" N VAL B 427 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 531 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1209 1.31 - 1.43: 2317 1.43 - 1.56: 4957 1.56 - 1.68: 124 1.68 - 1.81: 78 Bond restraints: 8685 Sorted by residual: bond pdb=" CB PLD A1001 " pdb=" O3 PLD A1001 " ideal model delta sigma weight residual 1.325 1.432 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" CB PLD B1001 " pdb=" O3 PLD B1001 " ideal model delta sigma weight residual 1.325 1.432 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" CB PLD C1001 " pdb=" O3 PLD C1001 " ideal model delta sigma weight residual 1.325 1.432 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C' PLD A1001 " pdb=" O2 PLD A1001 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C' PLD C1001 " pdb=" O2 PLD C1001 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 8680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 11563 3.45 - 6.90: 209 6.90 - 10.35: 15 10.35 - 13.80: 0 13.80 - 17.25: 3 Bond angle restraints: 11790 Sorted by residual: angle pdb=" O3P PLD C1001 " pdb=" P PLD C1001 " pdb=" O4P PLD C1001 " ideal model delta sigma weight residual 92.85 110.10 -17.25 3.00e+00 1.11e-01 3.30e+01 angle pdb=" O3P PLD A1001 " pdb=" P PLD A1001 " pdb=" O4P PLD A1001 " ideal model delta sigma weight residual 92.85 110.09 -17.24 3.00e+00 1.11e-01 3.30e+01 angle pdb=" O3P PLD B1001 " pdb=" P PLD B1001 " pdb=" O4P PLD B1001 " ideal model delta sigma weight residual 92.85 110.07 -17.22 3.00e+00 1.11e-01 3.30e+01 angle pdb=" C VAL A 235 " pdb=" N PHE A 236 " pdb=" CA PHE A 236 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C VAL B 235 " pdb=" N PHE B 236 " pdb=" CA PHE B 236 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 ... (remaining 11785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.22: 4818 32.22 - 64.45: 186 64.45 - 96.67: 21 96.67 - 128.89: 6 128.89 - 161.11: 9 Dihedral angle restraints: 5040 sinusoidal: 1989 harmonic: 3051 Sorted by residual: dihedral pdb=" OB PLD A1001 " pdb=" CB PLD A1001 " pdb=" O3 PLD A1001 " pdb=" C3 PLD A1001 " ideal model delta sinusoidal sigma weight residual -7.40 153.71 -161.11 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" OB PLD B1001 " pdb=" CB PLD B1001 " pdb=" O3 PLD B1001 " pdb=" C3 PLD B1001 " ideal model delta sinusoidal sigma weight residual -7.40 153.71 -161.11 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" OB PLD C1001 " pdb=" CB PLD C1001 " pdb=" O3 PLD C1001 " pdb=" C3 PLD C1001 " ideal model delta sinusoidal sigma weight residual -7.40 153.62 -161.02 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 5037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1045 0.048 - 0.097: 277 0.097 - 0.145: 31 0.145 - 0.193: 0 0.193 - 0.241: 3 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C2 PLD A1001 " pdb=" C1 PLD A1001 " pdb=" C3 PLD A1001 " pdb=" O2 PLD A1001 " both_signs ideal model delta sigma weight residual False -2.34 -2.58 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C2 PLD C1001 " pdb=" C1 PLD C1001 " pdb=" C3 PLD C1001 " pdb=" O2 PLD C1001 " both_signs ideal model delta sigma weight residual False -2.34 -2.58 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2 PLD B1001 " pdb=" C1 PLD B1001 " pdb=" C3 PLD B1001 " pdb=" O2 PLD B1001 " both_signs ideal model delta sigma weight residual False -2.34 -2.58 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1353 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 279 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 280 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 279 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO C 280 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 280 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 280 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 279 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 280 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " 0.027 5.00e-02 4.00e+02 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2715 2.84 - 3.36: 8344 3.36 - 3.87: 14980 3.87 - 4.39: 18813 4.39 - 4.90: 30406 Nonbonded interactions: 75258 Sorted by model distance: nonbonded pdb=" O GLU A 339 " pdb=" OG1 THR A 343 " model vdw 2.328 3.040 nonbonded pdb=" O GLU C 339 " pdb=" OG1 THR C 343 " model vdw 2.328 3.040 nonbonded pdb=" O GLU B 339 " pdb=" OG1 THR B 343 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR C 164 " pdb=" O HOH C1101 " model vdw 2.435 3.040 nonbonded pdb=" OG SER C 353 " pdb=" SG CYS C 379 " model vdw 2.441 3.400 ... (remaining 75253 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.170 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 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 : 0.008 0.107 8685 Z= 0.391 Angle : 0.955 17.245 11790 Z= 0.425 Chirality : 0.042 0.241 1356 Planarity : 0.005 0.048 1383 Dihedral : 18.691 161.115 3084 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.86 % Favored : 96.86 % Rotamer: Outliers : 0.98 % Allowed : 3.44 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.24), residues: 1050 helix: -0.73 (0.17), residues: 753 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.013 0.001 TYR A 184 PHE 0.016 0.002 PHE C 361 TRP 0.006 0.001 TRP B 300 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.39 ( 8685) covalent geometry : angle 0.95461 / 0.43 (11790) hydrogen bonds : bond 0.10732 / 7.39 ( 531) hydrogen bonds : angle 4.49842 / 3.24 ( 1584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.251 Fit side-chains REVERT: B 387 SER cc_start: 0.8367 (t) cc_final: 0.8135 (m) outliers start: 8 outliers final: 1 residues processed: 101 average time/residue: 0.3016 time to fit residues: 33.6111 Evaluate side-chains 79 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN C 415 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.110061 restraints weight = 9202.447| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.33 r_work: 0.2967 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8685 Z= 0.124 Angle : 0.545 8.545 11790 Z= 0.267 Chirality : 0.040 0.140 1356 Planarity : 0.005 0.052 1383 Dihedral : 20.293 176.716 1501 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.21 % Allowed : 8.24 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1050 helix: 0.59 (0.18), residues: 753 sheet: None (None), residues: 0 loop : -0.72 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 174 TYR 0.011 0.001 TYR A 184 PHE 0.016 0.001 PHE B 361 TRP 0.011 0.001 TRP C 108 HIS 0.002 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 ( 8685) covalent geometry : angle 0.54535 / 0.27 (11790) hydrogen bonds : bond 0.03768 / 2.52 ( 531) hydrogen bonds : angle 3.75312 / 2.76 ( 1584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.206 Fit side-chains REVERT: A 230 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7992 (mmmt) REVERT: A 387 SER cc_start: 0.8527 (t) cc_final: 0.8223 (m) REVERT: C 119 ILE cc_start: 0.8349 (mt) cc_final: 0.7943 (mp) REVERT: C 408 ILE cc_start: 0.8572 (mt) cc_final: 0.8210 (mt) REVERT: B 230 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8193 (mmmt) REVERT: B 387 SER cc_start: 0.8508 (t) cc_final: 0.8285 (m) REVERT: B 408 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8063 (mt) outliers start: 18 outliers final: 3 residues processed: 97 average time/residue: 0.2922 time to fit residues: 31.2171 Evaluate side-chains 87 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 408 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN A 416 ASN C 415 ASN B 415 ASN B 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.109557 restraints weight = 9179.369| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.33 r_work: 0.2952 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8685 Z= 0.136 Angle : 0.563 8.508 11790 Z= 0.273 Chirality : 0.041 0.163 1356 Planarity : 0.005 0.053 1383 Dihedral : 18.428 174.415 1500 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.85 % Allowed : 10.09 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1050 helix: 0.93 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -0.30 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.013 0.001 TYR A 184 PHE 0.024 0.002 PHE B 378 TRP 0.007 0.001 TRP C 108 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 8685) covalent geometry : angle 0.56275 / 0.27 (11790) hydrogen bonds : bond 0.03757 / 2.51 ( 531) hydrogen bonds : angle 3.75803 / 2.76 ( 1584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.300 Fit side-chains REVERT: A 230 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8030 (mmmt) REVERT: A 387 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8212 (m) REVERT: B 230 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8134 (mmmt) REVERT: B 387 SER cc_start: 0.8472 (t) cc_final: 0.8253 (m) outliers start: 15 outliers final: 4 residues processed: 90 average time/residue: 0.2989 time to fit residues: 29.7533 Evaluate side-chains 88 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 53 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 57 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 65.699 > 50:) chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 415 ASN B 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.135350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.107810 restraints weight = 9404.525| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.46 r_work: 0.2950 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8685 Z= 0.130 Angle : 0.552 8.417 11790 Z= 0.267 Chirality : 0.040 0.136 1356 Planarity : 0.005 0.054 1383 Dihedral : 16.364 155.675 1500 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.34 % Allowed : 11.32 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.26), residues: 1050 helix: 1.17 (0.19), residues: 759 sheet: None (None), residues: 0 loop : -0.21 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.012 0.001 TYR A 184 PHE 0.020 0.001 PHE B 378 TRP 0.009 0.001 TRP B 108 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 8685) covalent geometry : angle 0.55216 / 0.27 (11790) hydrogen bonds : bond 0.03647 / 2.43 ( 531) hydrogen bonds : angle 3.72644 / 2.74 ( 1584) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.285 Fit side-chains REVERT: A 230 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8036 (mmmt) REVERT: A 387 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8196 (m) REVERT: C 119 ILE cc_start: 0.8298 (mt) cc_final: 0.7866 (mp) REVERT: B 119 ILE cc_start: 0.8355 (mt) cc_final: 0.7930 (mp) REVERT: B 230 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8049 (mmmt) REVERT: B 387 SER cc_start: 0.8486 (t) cc_final: 0.8229 (m) REVERT: B 408 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8025 (mt) outliers start: 19 outliers final: 6 residues processed: 101 average time/residue: 0.3051 time to fit residues: 34.1654 Evaluate side-chains 91 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 408 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 72 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN A 416 ASN C 415 ASN B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.136744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.109320 restraints weight = 9330.272| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.45 r_work: 0.2968 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8685 Z= 0.121 Angle : 0.551 8.520 11790 Z= 0.265 Chirality : 0.041 0.167 1356 Planarity : 0.005 0.047 1383 Dihedral : 14.157 111.719 1500 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.60 % Allowed : 12.42 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1050 helix: 1.33 (0.19), residues: 759 sheet: None (None), residues: 0 loop : -0.19 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.011 0.001 TYR C 184 PHE 0.019 0.001 PHE A 378 TRP 0.007 0.001 TRP B 108 HIS 0.003 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 8685) covalent geometry : angle 0.55083 / 0.27 (11790) hydrogen bonds : bond 0.03563 / 2.39 ( 531) hydrogen bonds : angle 3.73300 / 2.74 ( 1584) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.307 Fit side-chains REVERT: A 119 ILE cc_start: 0.8311 (mt) cc_final: 0.7866 (mp) REVERT: A 230 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8048 (mmmt) REVERT: A 387 SER cc_start: 0.8446 (t) cc_final: 0.8165 (m) REVERT: B 230 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8048 (mmmt) REVERT: B 387 SER cc_start: 0.8400 (t) cc_final: 0.8174 (m) outliers start: 13 outliers final: 3 residues processed: 94 average time/residue: 0.3257 time to fit residues: 33.7314 Evaluate side-chains 86 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain B residue 230 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 3 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 ASN C 415 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.104770 restraints weight = 9300.341| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.35 r_work: 0.2919 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8685 Z= 0.174 Angle : 0.608 8.885 11790 Z= 0.293 Chirality : 0.043 0.223 1356 Planarity : 0.005 0.046 1383 Dihedral : 13.671 87.674 1500 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.46 % Allowed : 12.42 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.26), residues: 1050 helix: 1.13 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.08 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.015 0.002 TYR A 184 PHE 0.023 0.002 PHE A 378 TRP 0.007 0.001 TRP B 400 HIS 0.004 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.17 ( 8685) covalent geometry : angle 0.60769 / 0.29 (11790) hydrogen bonds : bond 0.03954 / 2.64 ( 531) hydrogen bonds : angle 3.88985 / 2.85 ( 1584) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.189 Fit side-chains REVERT: A 230 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8137 (mmmt) REVERT: A 387 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8301 (m) REVERT: A 408 ILE cc_start: 0.8687 (mt) cc_final: 0.8444 (mt) REVERT: C 119 ILE cc_start: 0.8416 (mt) cc_final: 0.7996 (mp) REVERT: C 215 MET cc_start: 0.8639 (mtp) cc_final: 0.8386 (mtm) REVERT: B 230 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8134 (mmmt) REVERT: B 387 SER cc_start: 0.8580 (t) cc_final: 0.8309 (m) outliers start: 20 outliers final: 7 residues processed: 98 average time/residue: 0.3293 time to fit residues: 35.7268 Evaluate side-chains 94 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 415 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.135889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.108316 restraints weight = 9414.619| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.46 r_work: 0.2947 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 0.039 8685 Z= 0.131 Angle : 0.563 8.829 11790 Z= 0.271 Chirality : 0.041 0.236 1356 Planarity : 0.005 0.046 1383 Dihedral : 12.877 89.450 1500 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.46 % Allowed : 12.67 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1050 helix: 1.29 (0.19), residues: 759 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 174 TYR 0.011 0.001 TYR A 184 PHE 0.020 0.001 PHE A 378 TRP 0.013 0.001 TRP B 108 HIS 0.003 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 8685) covalent geometry : angle 0.56308 / 0.27 (11790) hydrogen bonds : bond 0.03638 / 2.43 ( 531) hydrogen bonds : angle 3.81221 / 2.80 ( 1584) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.269 Fit side-chains REVERT: A 230 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8037 (mmmt) REVERT: A 387 SER cc_start: 0.8482 (OUTLIER) cc_final: 0.8188 (m) REVERT: B 119 ILE cc_start: 0.8388 (mt) cc_final: 0.7967 (mp) REVERT: B 230 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8046 (mmmt) REVERT: B 387 SER cc_start: 0.8463 (t) cc_final: 0.8216 (m) outliers start: 20 outliers final: 7 residues processed: 100 average time/residue: 0.2941 time to fit residues: 32.5620 Evaluate side-chains 91 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 13 optimal weight: 0.0370 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 ASN C 415 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.137323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.111201 restraints weight = 9386.100| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.31 r_work: 0.3018 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8685 Z= 0.110 Angle : 0.539 8.513 11790 Z= 0.261 Chirality : 0.040 0.173 1356 Planarity : 0.005 0.047 1383 Dihedral : 12.111 88.278 1500 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.97 % Allowed : 13.41 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.26), residues: 1050 helix: 1.52 (0.19), residues: 759 sheet: None (None), residues: 0 loop : -0.16 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.008 0.001 TYR C 184 PHE 0.025 0.001 PHE A 378 TRP 0.012 0.001 TRP B 108 HIS 0.002 0.000 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 8685) covalent geometry : angle 0.53922 / 0.26 (11790) hydrogen bonds : bond 0.03412 / 2.29 ( 531) hydrogen bonds : angle 3.74698 / 2.74 ( 1584) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.286 Fit side-chains REVERT: A 119 ILE cc_start: 0.8425 (mt) cc_final: 0.7996 (mp) REVERT: A 187 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8528 (tpp) REVERT: A 230 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8138 (mmmt) REVERT: A 387 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8167 (m) REVERT: C 119 ILE cc_start: 0.8487 (mt) cc_final: 0.8105 (mp) REVERT: B 119 ILE cc_start: 0.8491 (mt) cc_final: 0.8084 (mp) REVERT: B 230 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8158 (mmmt) outliers start: 16 outliers final: 7 residues processed: 104 average time/residue: 0.2991 time to fit residues: 34.3892 Evaluate side-chains 100 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.0370 chunk 83 optimal weight: 0.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 ASN C 415 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.143460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117775 restraints weight = 9325.612| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.35 r_work: 0.3044 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8685 Z= 0.103 Angle : 0.539 8.398 11790 Z= 0.260 Chirality : 0.040 0.205 1356 Planarity : 0.005 0.046 1383 Dihedral : 11.636 88.529 1500 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.60 % Allowed : 14.15 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.26), residues: 1050 helix: 1.65 (0.19), residues: 759 sheet: None (None), residues: 0 loop : -0.16 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.007 0.001 TYR C 184 PHE 0.031 0.001 PHE A 378 TRP 0.014 0.001 TRP B 346 HIS 0.002 0.000 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 8685) covalent geometry : angle 0.53941 / 0.26 (11790) hydrogen bonds : bond 0.03290 / 2.20 ( 531) hydrogen bonds : angle 3.73167 / 2.72 ( 1584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.205 Fit side-chains REVERT: A 119 ILE cc_start: 0.8355 (mt) cc_final: 0.7927 (mp) REVERT: A 187 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8544 (tpp) REVERT: C 119 ILE cc_start: 0.8412 (mt) cc_final: 0.8018 (mp) REVERT: C 193 MET cc_start: 0.8975 (mtp) cc_final: 0.8764 (mtp) REVERT: B 119 ILE cc_start: 0.8443 (mt) cc_final: 0.8028 (mp) REVERT: B 230 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8162 (mmmt) outliers start: 13 outliers final: 5 residues processed: 104 average time/residue: 0.2947 time to fit residues: 33.8627 Evaluate side-chains 98 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 ASN B 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.131281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.103589 restraints weight = 9359.479| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.40 r_work: 0.2909 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8685 Z= 0.189 Angle : 0.634 10.553 11790 Z= 0.306 Chirality : 0.044 0.223 1356 Planarity : 0.005 0.044 1383 Dihedral : 12.781 89.421 1500 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.35 % Allowed : 14.64 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1050 helix: 1.27 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.03 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 124 TYR 0.016 0.002 TYR C 184 PHE 0.042 0.002 PHE A 378 TRP 0.013 0.001 TRP B 346 HIS 0.005 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 ( 8685) covalent geometry : angle 0.63420 / 0.31 (11790) hydrogen bonds : bond 0.04038 / 2.69 ( 531) hydrogen bonds : angle 3.96869 / 2.90 ( 1584) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.259 Fit side-chains REVERT: A 408 ILE cc_start: 0.8673 (mt) cc_final: 0.8448 (mt) REVERT: C 119 ILE cc_start: 0.8387 (mt) cc_final: 0.7967 (mp) REVERT: C 193 MET cc_start: 0.9190 (mtp) cc_final: 0.8932 (mtp) REVERT: C 408 ILE cc_start: 0.8604 (mt) cc_final: 0.8345 (mt) REVERT: B 230 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8156 (mmmt) outliers start: 11 outliers final: 7 residues processed: 92 average time/residue: 0.3305 time to fit residues: 33.3181 Evaluate side-chains 90 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 415 ASN B 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.136936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109926 restraints weight = 9293.065| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.38 r_work: 0.2957 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8685 Z= 0.137 Angle : 0.589 9.538 11790 Z= 0.284 Chirality : 0.042 0.209 1356 Planarity : 0.005 0.045 1383 Dihedral : 12.177 87.151 1500 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.23 % Allowed : 15.01 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.26), residues: 1050 helix: 1.36 (0.19), residues: 759 sheet: None (None), residues: 0 loop : -0.17 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.011 0.001 TYR A 184 PHE 0.038 0.002 PHE A 378 TRP 0.015 0.001 TRP B 346 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 8685) covalent geometry : angle 0.58930 / 0.28 (11790) hydrogen bonds : bond 0.03673 / 2.46 ( 531) hydrogen bonds : angle 3.87879 / 2.83 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.68 seconds wall clock time: 35 minutes 29.38 seconds (2129.38 seconds total)