Starting phenix.real_space_refine on Tue Feb 3 20:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6d_49057/02_2026/9n6d_49057.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6d_49057/02_2026/9n6d_49057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n6d_49057/02_2026/9n6d_49057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6d_49057/02_2026/9n6d_49057.map" model { file = "/net/cci-nas-00/data/ceres_data/9n6d_49057/02_2026/9n6d_49057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6d_49057/02_2026/9n6d_49057.cif" } resolution = 3.03 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4130 2.51 5 N 1080 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6458 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3229 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 377} Chain: "B" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3229 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 377} Time building chain proxies: 1.62, per 1000 atoms: 0.25 Number of scatterers: 6458 At special positions: 0 Unit cell: (158.032, 56.44, 77.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1216 8.00 N 1080 7.00 C 4130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 403 " distance=2.03 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 403 " distance=2.03 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: 0.62 Conformation dependent library (CDL) restraints added in 236.5 milliseconds 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 2 sheets defined 68.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 13 through 27 Processing helix chain 'A' and resid 34 through 47 Processing helix chain 'A' and resid 49 through 65 removed outlier: 4.420A pdb=" N VAL A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.936A pdb=" N THR A 104 " --> pdb=" O HIS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 160 through 173 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 200 through 219 removed outlier: 3.559A pdb=" N ASN A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 removed outlier: 3.645A pdb=" N ASP A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.686A pdb=" N PHE A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 288 removed outlier: 3.635A pdb=" N PHE A 286 " --> pdb=" O TRP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 290 No H-bonds generated for 'chain 'A' and resid 289 through 290' Processing helix chain 'A' and resid 291 through 295 removed outlier: 3.759A pdb=" N LEU A 295 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 316 through 327 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 338 through 339 No H-bonds generated for 'chain 'A' and resid 338 through 339' Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 352 through 368 Processing helix chain 'A' and resid 375 through 406 removed outlier: 3.686A pdb=" N LEU A 381 " --> pdb=" O CYS A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 27 Processing helix chain 'B' and resid 34 through 48 Processing helix chain 'B' and resid 49 through 66 removed outlier: 4.006A pdb=" N VAL B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 60 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 130 through 134 removed outlier: 3.865A pdb=" N PHE B 134 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 160 through 173 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 200 through 219 Processing helix chain 'B' and resid 238 through 249 Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 266 through 289 removed outlier: 3.524A pdb=" N GLY B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 removed outlier: 5.294A pdb=" N PHE B 293 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 295 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 313 Processing helix chain 'B' and resid 316 through 327 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 338 through 339 No H-bonds generated for 'chain 'B' and resid 338 through 339' Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 352 through 368 Processing helix chain 'B' and resid 375 through 406 removed outlier: 3.905A pdb=" N GLU B 379 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114 removed outlier: 6.572A pdb=" N LEU A 69 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N TRP A 124 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A 71 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU A 126 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 73 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ASN A 70 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N ILE A 152 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA A 72 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE A 154 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR A 74 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.669A pdb=" N LEU B 69 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N TRP B 124 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 71 " --> pdb=" O TRP B 124 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU B 126 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 73 " --> pdb=" O LEU B 126 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1098 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: 0.95 Time building geometry restraints manager: 0.80 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: 2036 1.34 - 1.46: 948 1.46 - 1.58: 3560 1.58 - 1.70: 0 1.70 - 1.81: 52 Bond restraints: 6596 Sorted by residual: bond pdb=" N ILE B 329 " pdb=" CA ILE B 329 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.65e+00 bond pdb=" N ILE B 353 " pdb=" CA ILE B 353 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.69e+00 bond pdb=" N VAL B 53 " pdb=" CA VAL B 53 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.21e-02 6.83e+03 7.65e+00 bond pdb=" N THR B 74 " pdb=" CA THR B 74 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.65e+00 bond pdb=" N ILE B 50 " pdb=" CA ILE B 50 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.23e-02 6.61e+03 7.59e+00 ... (remaining 6591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 8499 1.72 - 3.44: 345 3.44 - 5.16: 43 5.16 - 6.88: 7 6.88 - 8.60: 6 Bond angle restraints: 8900 Sorted by residual: angle pdb=" N HIS B 376 " pdb=" CA HIS B 376 " pdb=" C HIS B 376 " ideal model delta sigma weight residual 113.50 106.56 6.94 1.23e+00 6.61e-01 3.19e+01 angle pdb=" N HIS B 236 " pdb=" CA HIS B 236 " pdb=" C HIS B 236 " ideal model delta sigma weight residual 110.53 117.78 -7.25 1.29e+00 6.01e-01 3.16e+01 angle pdb=" N HIS A 236 " pdb=" CA HIS A 236 " pdb=" C HIS A 236 " ideal model delta sigma weight residual 110.36 117.51 -7.15 1.55e+00 4.16e-01 2.13e+01 angle pdb=" CA THR B 352 " pdb=" C THR B 352 " pdb=" O THR B 352 " ideal model delta sigma weight residual 122.27 118.04 4.23 1.16e+00 7.43e-01 1.33e+01 angle pdb=" N THR B 352 " pdb=" CA THR B 352 " pdb=" C THR B 352 " ideal model delta sigma weight residual 111.17 106.07 5.10 1.41e+00 5.03e-01 1.31e+01 ... (remaining 8895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 3608 14.64 - 29.27: 296 29.27 - 43.91: 80 43.91 - 58.55: 28 58.55 - 73.18: 6 Dihedral angle restraints: 4018 sinusoidal: 1704 harmonic: 2314 Sorted by residual: dihedral pdb=" CB CYS B 235 " pdb=" SG CYS B 235 " pdb=" SG CYS B 403 " pdb=" CB CYS B 403 " ideal model delta sinusoidal sigma weight residual 93.00 163.86 -70.86 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS A 235 " pdb=" SG CYS A 235 " pdb=" SG CYS A 403 " pdb=" CB CYS A 403 " ideal model delta sinusoidal sigma weight residual 93.00 158.38 -65.38 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CA PRO A 251 " pdb=" C PRO A 251 " pdb=" N VAL A 252 " pdb=" CA VAL A 252 " ideal model delta harmonic sigma weight residual -180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 616 0.038 - 0.075: 233 0.075 - 0.113: 96 0.113 - 0.150: 21 0.150 - 0.187: 8 Chirality restraints: 974 Sorted by residual: chirality pdb=" CA ILE B 329 " pdb=" N ILE B 329 " pdb=" C ILE B 329 " pdb=" CB ILE B 329 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA ILE B 43 " pdb=" N ILE B 43 " pdb=" C ILE B 43 " pdb=" CB ILE B 43 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 971 not shown) Planarity restraints: 1152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 235 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C CYS B 235 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS B 235 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS B 236 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 235 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C CYS A 235 " -0.039 2.00e-02 2.50e+03 pdb=" O CYS A 235 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS A 236 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 128 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C GLY A 128 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY A 128 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 129 " -0.013 2.00e-02 2.50e+03 ... (remaining 1149 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1416 2.78 - 3.31: 6358 3.31 - 3.84: 10239 3.84 - 4.37: 12075 4.37 - 4.90: 20445 Nonbonded interactions: 50533 Sorted by model distance: nonbonded pdb=" OG SER B 341 " pdb=" OD2 ASP B 394 " model vdw 2.254 3.040 nonbonded pdb=" ND2 ASN A 31 " pdb=" OD1 ASN A 368 " model vdw 2.264 3.120 nonbonded pdb=" NH2 ARG B 201 " pdb=" OH TYR B 237 " model vdw 2.299 3.120 nonbonded pdb=" NE2 GLN A 13 " pdb=" OD1 ASP A 14 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASN B 264 " pdb=" NZ LYS B 273 " model vdw 2.313 3.120 ... (remaining 50528 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: 0.01 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: 7.300 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6598 Z= 0.336 Angle : 0.762 8.597 8904 Z= 0.501 Chirality : 0.049 0.187 974 Planarity : 0.004 0.047 1152 Dihedral : 12.485 73.185 2508 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.42 % Allowed : 8.17 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.46 (0.30), residues: 784 helix: 1.66 (0.24), residues: 484 sheet: 0.56 (0.63), residues: 74 loop : -0.33 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 181 TYR 0.034 0.002 TYR B 139 PHE 0.014 0.001 PHE B 216 TRP 0.009 0.001 TRP B 279 HIS 0.007 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 6596) covalent geometry : angle 0.75893 ( 8900) SS BOND : bond 0.00049 ( 2) SS BOND : angle 3.33611 ( 4) hydrogen bonds : bond 0.18026 ( 381) hydrogen bonds : angle 5.62703 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.276 Fit side-chains REVERT: B 376 HIS cc_start: 0.6660 (OUTLIER) cc_final: 0.6214 (t70) outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 0.0974 time to fit residues: 7.0191 Evaluate side-chains 41 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain B residue 376 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 51 GLN B 93 HIS B 162 ASN B 236 HIS B 376 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.106899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073545 restraints weight = 15173.106| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 4.01 r_work: 0.2980 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6598 Z= 0.185 Angle : 0.552 5.772 8904 Z= 0.295 Chirality : 0.042 0.148 974 Planarity : 0.004 0.041 1152 Dihedral : 4.658 40.529 858 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.66 % Allowed : 6.79 % Favored : 91.55 % 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: 1.75 (0.30), residues: 784 helix: 2.07 (0.23), residues: 488 sheet: 0.26 (0.62), residues: 72 loop : -0.53 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 325 TYR 0.013 0.002 TYR B 139 PHE 0.014 0.001 PHE A 134 TRP 0.007 0.001 TRP B 279 HIS 0.007 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 6596) covalent geometry : angle 0.55076 ( 8900) SS BOND : bond 0.00135 ( 2) SS BOND : angle 1.57694 ( 4) hydrogen bonds : bond 0.05750 ( 381) hydrogen bonds : angle 4.08130 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.259 Fit side-chains REVERT: A 158 ARG cc_start: 0.8770 (mtp-110) cc_final: 0.8169 (mtp85) REVERT: B 118 MET cc_start: 0.7962 (mmm) cc_final: 0.7526 (mtp) REVERT: B 215 THR cc_start: 0.8585 (m) cc_final: 0.7948 (m) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 0.0790 time to fit residues: 6.1435 Evaluate side-chains 47 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 265 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.106208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.072279 restraints weight = 15107.621| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.04 r_work: 0.2955 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6598 Z= 0.172 Angle : 0.521 6.059 8904 Z= 0.277 Chirality : 0.041 0.153 974 Planarity : 0.004 0.037 1152 Dihedral : 4.364 37.255 856 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.80 % Allowed : 7.06 % Favored : 91.14 % 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: 1.99 (0.30), residues: 784 helix: 2.36 (0.23), residues: 488 sheet: 0.18 (0.64), residues: 72 loop : -0.67 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 158 TYR 0.014 0.002 TYR B 139 PHE 0.011 0.001 PHE A 216 TRP 0.006 0.001 TRP B 279 HIS 0.009 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 6596) covalent geometry : angle 0.52058 ( 8900) SS BOND : bond 0.00056 ( 2) SS BOND : angle 1.19825 ( 4) hydrogen bonds : bond 0.05381 ( 381) hydrogen bonds : angle 3.79816 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.328 Fit side-chains REVERT: A 158 ARG cc_start: 0.8882 (mtp-110) cc_final: 0.8340 (mtp85) REVERT: B 118 MET cc_start: 0.7995 (mmm) cc_final: 0.7691 (mtp) REVERT: B 216 PHE cc_start: 0.8693 (m-80) cc_final: 0.8270 (m-80) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 0.1084 time to fit residues: 7.0954 Evaluate side-chains 45 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.107454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073258 restraints weight = 15162.389| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 4.15 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6598 Z= 0.123 Angle : 0.475 6.788 8904 Z= 0.252 Chirality : 0.039 0.147 974 Planarity : 0.003 0.036 1152 Dihedral : 4.214 35.573 856 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.66 % Allowed : 6.93 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.28 (0.30), residues: 784 helix: 2.62 (0.23), residues: 488 sheet: 0.25 (0.66), residues: 72 loop : -0.62 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.011 0.001 TYR B 139 PHE 0.011 0.001 PHE A 134 TRP 0.004 0.001 TRP B 279 HIS 0.004 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6596) covalent geometry : angle 0.47505 ( 8900) SS BOND : bond 0.00061 ( 2) SS BOND : angle 1.06771 ( 4) hydrogen bonds : bond 0.04488 ( 381) hydrogen bonds : angle 3.56807 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.269 Fit side-chains REVERT: A 158 ARG cc_start: 0.8362 (mtp-110) cc_final: 0.8039 (mtp-110) REVERT: A 216 PHE cc_start: 0.8488 (m-80) cc_final: 0.8149 (m-80) REVERT: B 118 MET cc_start: 0.7925 (mmm) cc_final: 0.7609 (mtp) REVERT: B 154 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8412 (tp) REVERT: B 216 PHE cc_start: 0.8699 (m-80) cc_final: 0.8354 (m-80) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 0.0939 time to fit residues: 6.0718 Evaluate side-chains 44 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 72 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.106946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072823 restraints weight = 15354.376| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 4.14 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6598 Z= 0.126 Angle : 0.461 6.076 8904 Z= 0.241 Chirality : 0.039 0.150 974 Planarity : 0.003 0.036 1152 Dihedral : 4.169 34.466 856 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.39 % Allowed : 7.48 % Favored : 91.14 % 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: 2.37 (0.31), residues: 784 helix: 2.71 (0.23), residues: 488 sheet: 0.24 (0.67), residues: 72 loop : -0.59 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.009 0.001 TYR B 139 PHE 0.010 0.001 PHE A 134 TRP 0.004 0.001 TRP B 279 HIS 0.004 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6596) covalent geometry : angle 0.46087 ( 8900) SS BOND : bond 0.00058 ( 2) SS BOND : angle 1.05494 ( 4) hydrogen bonds : bond 0.04473 ( 381) hydrogen bonds : angle 3.48756 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.340 Fit side-chains REVERT: A 158 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.7683 (ttt-90) REVERT: A 216 PHE cc_start: 0.8378 (m-80) cc_final: 0.8142 (m-80) REVERT: B 118 MET cc_start: 0.7928 (mmm) cc_final: 0.7623 (mtp) REVERT: B 154 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8452 (tp) REVERT: B 216 PHE cc_start: 0.8745 (m-80) cc_final: 0.8387 (m-80) outliers start: 10 outliers final: 5 residues processed: 47 average time/residue: 0.0864 time to fit residues: 5.5657 Evaluate side-chains 45 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 265 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 14 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.107598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073594 restraints weight = 15253.346| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 4.14 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6598 Z= 0.110 Angle : 0.466 7.738 8904 Z= 0.244 Chirality : 0.039 0.146 974 Planarity : 0.003 0.035 1152 Dihedral : 3.906 30.797 854 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.52 % Allowed : 8.45 % Favored : 90.03 % 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: 2.48 (0.31), residues: 784 helix: 2.81 (0.23), residues: 488 sheet: 0.29 (0.67), residues: 72 loop : -0.59 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 158 TYR 0.009 0.001 TYR B 139 PHE 0.010 0.001 PHE A 134 TRP 0.003 0.001 TRP B 279 HIS 0.003 0.000 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6596) covalent geometry : angle 0.46611 ( 8900) SS BOND : bond 0.00060 ( 2) SS BOND : angle 0.97804 ( 4) hydrogen bonds : bond 0.04180 ( 381) hydrogen bonds : angle 3.43490 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.273 Fit side-chains REVERT: A 111 HIS cc_start: 0.7674 (t-90) cc_final: 0.7019 (t-90) REVERT: A 158 ARG cc_start: 0.8425 (mtp-110) cc_final: 0.7713 (ttt-90) REVERT: A 216 PHE cc_start: 0.8377 (m-80) cc_final: 0.8127 (m-80) REVERT: B 118 MET cc_start: 0.7908 (mmm) cc_final: 0.7594 (mtp) REVERT: B 154 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8477 (tp) REVERT: B 216 PHE cc_start: 0.8747 (m-80) cc_final: 0.8364 (m-80) outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 0.0876 time to fit residues: 5.9486 Evaluate side-chains 46 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.107113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073274 restraints weight = 15336.016| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.10 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6598 Z= 0.120 Angle : 0.481 12.400 8904 Z= 0.247 Chirality : 0.039 0.144 974 Planarity : 0.003 0.037 1152 Dihedral : 3.906 31.271 854 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.39 % Allowed : 9.00 % Favored : 89.61 % 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: 2.48 (0.31), residues: 784 helix: 2.82 (0.23), residues: 488 sheet: 0.30 (0.68), residues: 72 loop : -0.62 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 158 TYR 0.011 0.001 TYR A 139 PHE 0.009 0.001 PHE A 134 TRP 0.004 0.001 TRP B 279 HIS 0.004 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6596) covalent geometry : angle 0.48021 ( 8900) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.95573 ( 4) hydrogen bonds : bond 0.04293 ( 381) hydrogen bonds : angle 3.46034 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.283 Fit side-chains REVERT: A 111 HIS cc_start: 0.7705 (t-90) cc_final: 0.7062 (t-90) REVERT: A 158 ARG cc_start: 0.8486 (mtp-110) cc_final: 0.7734 (mmm-85) REVERT: A 216 PHE cc_start: 0.8435 (m-80) cc_final: 0.8140 (m-80) REVERT: B 32 ILE cc_start: 0.8637 (mt) cc_final: 0.8411 (mm) REVERT: B 118 MET cc_start: 0.7910 (mmm) cc_final: 0.7667 (mtp) REVERT: B 154 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8481 (tp) REVERT: B 211 ASN cc_start: 0.9281 (m-40) cc_final: 0.9054 (m-40) REVERT: B 216 PHE cc_start: 0.8796 (m-80) cc_final: 0.8374 (m-80) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.0884 time to fit residues: 5.9286 Evaluate side-chains 53 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 388 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 0.0570 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 45 optimal weight: 0.0670 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.108363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074439 restraints weight = 15330.888| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.13 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6598 Z= 0.100 Angle : 0.475 10.882 8904 Z= 0.242 Chirality : 0.038 0.147 974 Planarity : 0.003 0.036 1152 Dihedral : 3.807 32.077 854 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.66 % Allowed : 8.59 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.63 (0.31), residues: 784 helix: 2.94 (0.23), residues: 488 sheet: 0.31 (0.68), residues: 72 loop : -0.56 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 158 TYR 0.009 0.001 TYR B 139 PHE 0.008 0.001 PHE A 134 TRP 0.003 0.001 TRP B 124 HIS 0.003 0.000 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 6596) covalent geometry : angle 0.47462 ( 8900) SS BOND : bond 0.00072 ( 2) SS BOND : angle 0.92540 ( 4) hydrogen bonds : bond 0.03746 ( 381) hydrogen bonds : angle 3.33514 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.271 Fit side-chains REVERT: A 111 HIS cc_start: 0.7743 (t-90) cc_final: 0.7098 (t-90) REVERT: A 158 ARG cc_start: 0.8500 (mtp-110) cc_final: 0.8087 (mtp-110) REVERT: A 216 PHE cc_start: 0.8443 (m-80) cc_final: 0.8141 (m-80) REVERT: B 32 ILE cc_start: 0.8606 (mt) cc_final: 0.8380 (mm) REVERT: B 118 MET cc_start: 0.7888 (mmm) cc_final: 0.7587 (mtp) REVERT: B 154 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8459 (tp) REVERT: B 158 ARG cc_start: 0.8729 (mmp80) cc_final: 0.8368 (mmp80) outliers start: 12 outliers final: 9 residues processed: 46 average time/residue: 0.0881 time to fit residues: 5.6289 Evaluate side-chains 48 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 265 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.107815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073430 restraints weight = 15429.446| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.23 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6598 Z= 0.111 Angle : 0.471 7.932 8904 Z= 0.243 Chirality : 0.039 0.146 974 Planarity : 0.003 0.036 1152 Dihedral : 3.811 32.106 854 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.39 % Allowed : 8.73 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.69 (0.31), residues: 784 helix: 2.98 (0.23), residues: 488 sheet: 0.30 (0.68), residues: 72 loop : -0.52 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 274 TYR 0.010 0.001 TYR B 139 PHE 0.008 0.001 PHE B 216 TRP 0.003 0.001 TRP B 124 HIS 0.004 0.000 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6596) covalent geometry : angle 0.47083 ( 8900) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.93178 ( 4) hydrogen bonds : bond 0.04016 ( 381) hydrogen bonds : angle 3.39007 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.308 Fit side-chains REVERT: A 32 ILE cc_start: 0.8603 (mt) cc_final: 0.8365 (mm) REVERT: A 111 HIS cc_start: 0.7711 (t-90) cc_final: 0.7043 (t-90) REVERT: A 158 ARG cc_start: 0.8521 (mtp-110) cc_final: 0.8102 (mtp-110) REVERT: B 32 ILE cc_start: 0.8610 (mt) cc_final: 0.8381 (mm) REVERT: B 118 MET cc_start: 0.7862 (mmm) cc_final: 0.7579 (mtp) REVERT: B 154 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8420 (tp) REVERT: B 216 PHE cc_start: 0.8709 (m-80) cc_final: 0.8427 (m-80) outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.0916 time to fit residues: 5.9895 Evaluate side-chains 50 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 265 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.105583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.073038 restraints weight = 15034.615| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.96 r_work: 0.2990 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6598 Z= 0.135 Angle : 0.496 9.196 8904 Z= 0.254 Chirality : 0.039 0.144 974 Planarity : 0.003 0.036 1152 Dihedral : 3.886 32.032 854 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.52 % Allowed : 8.59 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.63 (0.31), residues: 784 helix: 2.96 (0.23), residues: 488 sheet: 0.20 (0.68), residues: 72 loop : -0.58 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.012 0.001 TYR B 139 PHE 0.008 0.001 PHE B 216 TRP 0.004 0.001 TRP B 279 HIS 0.004 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6596) covalent geometry : angle 0.49542 ( 8900) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.93800 ( 4) hydrogen bonds : bond 0.04372 ( 381) hydrogen bonds : angle 3.43689 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.274 Fit side-chains REVERT: A 111 HIS cc_start: 0.7865 (t-90) cc_final: 0.7261 (t-90) REVERT: A 158 ARG cc_start: 0.9063 (mtp-110) cc_final: 0.8707 (mtp-110) REVERT: B 32 ILE cc_start: 0.8749 (mt) cc_final: 0.8528 (mm) REVERT: B 118 MET cc_start: 0.8202 (mmm) cc_final: 0.7948 (mtp) REVERT: B 137 LYS cc_start: 0.8279 (tptm) cc_final: 0.8074 (tptp) REVERT: B 154 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8675 (tp) REVERT: B 158 ARG cc_start: 0.8696 (mmp80) cc_final: 0.8346 (mmm160) REVERT: B 216 PHE cc_start: 0.8693 (m-80) cc_final: 0.8239 (m-80) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 0.0909 time to fit residues: 5.5587 Evaluate side-chains 48 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 265 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.0670 chunk 57 optimal weight: 8.9990 chunk 51 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.109515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.075861 restraints weight = 15852.433| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 4.07 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6598 Z= 0.100 Angle : 0.474 8.423 8904 Z= 0.244 Chirality : 0.039 0.144 974 Planarity : 0.003 0.034 1152 Dihedral : 3.804 32.408 854 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.25 % Allowed : 9.14 % Favored : 89.61 % 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: 2.75 (0.31), residues: 784 helix: 3.05 (0.23), residues: 488 sheet: 0.28 (0.68), residues: 72 loop : -0.52 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 158 TYR 0.010 0.001 TYR B 139 PHE 0.007 0.001 PHE A 134 TRP 0.003 0.001 TRP B 124 HIS 0.003 0.000 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 6596) covalent geometry : angle 0.47414 ( 8900) SS BOND : bond 0.00059 ( 2) SS BOND : angle 0.89171 ( 4) hydrogen bonds : bond 0.03737 ( 381) hydrogen bonds : angle 3.35163 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1688.47 seconds wall clock time: 29 minutes 47.32 seconds (1787.32 seconds total)