Starting phenix.real_space_refine on Wed Mar 12 14:05:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xde_38275/03_2025/8xde_38275_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xde_38275/03_2025/8xde_38275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xde_38275/03_2025/8xde_38275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xde_38275/03_2025/8xde_38275.map" model { file = "/net/cci-nas-00/data/ceres_data/8xde_38275/03_2025/8xde_38275_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xde_38275/03_2025/8xde_38275_neut.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 54 5.16 5 C 5349 2.51 5 N 1227 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8010 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2670 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 19, 'TRANS': 325} Restraints were copied for chains: C, B Time building chain proxies: 5.01, per 1000 atoms: 0.63 Number of scatterers: 8010 At special positions: 0 Unit cell: (97.58, 93.48, 69.7, 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 54 16.00 O 1380 8.00 N 1227 7.00 C 5349 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 77.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... 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 179 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 229 removed outlier: 3.915A pdb=" N CYS A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.661A pdb=" N ILE A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'A' and resid 278 through 292 removed outlier: 4.031A 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 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.618A pdb=" N SER A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 334 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.628A pdb=" N THR A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 365 through 392 removed outlier: 3.864A pdb=" N VAL A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.505A pdb=" N VAL A 427 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 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 179 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 229 removed outlier: 3.915A pdb=" N CYS B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) Proline residue: B 218 - end of helix removed outlier: 3.661A pdb=" N ILE B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 237 through 252 Processing helix chain 'B' and resid 278 through 292 removed outlier: 4.033A 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 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 313 removed outlier: 3.620A pdb=" N SER B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 334 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.630A pdb=" N THR B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 365 through 392 removed outlier: 3.865A pdb=" N VAL B 392 " --> pdb=" O ASN B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.505A pdb=" N VAL B 427 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 440 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 179 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 229 removed outlier: 3.913A pdb=" N CYS C 217 " --> pdb=" O THR C 213 " (cutoff:3.500A) Proline residue: C 218 - end of helix removed outlier: 3.661A pdb=" N ILE C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 237 through 252 Processing helix chain 'C' and resid 278 through 292 removed outlier: 4.031A 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 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 298 through 313 removed outlier: 3.620A pdb=" N SER C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 334 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.628A pdb=" N THR C 343 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 358 Processing helix chain 'C' and resid 365 through 392 removed outlier: 3.865A pdb=" N VAL C 392 " --> pdb=" O ASN C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 423 through 427 removed outlier: 3.505A pdb=" N VAL C 427 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 440 525 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 2.25 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: 2355 1.34 - 1.46: 1832 1.46 - 1.57: 3982 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 8253 Sorted by residual: bond pdb=" CA PHE A 236 " pdb=" CB PHE A 236 " ideal model delta sigma weight residual 1.530 1.504 0.026 1.69e-02 3.50e+03 2.37e+00 bond pdb=" CA PHE C 236 " pdb=" CB PHE C 236 " ideal model delta sigma weight residual 1.530 1.505 0.025 1.69e-02 3.50e+03 2.27e+00 bond pdb=" CA PHE B 236 " pdb=" CB PHE B 236 " ideal model delta sigma weight residual 1.530 1.505 0.025 1.69e-02 3.50e+03 2.22e+00 bond pdb=" CA VAL A 235 " pdb=" CB VAL A 235 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.34e-02 5.57e+03 8.42e-01 bond pdb=" CA VAL C 235 " pdb=" CB VAL C 235 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.34e-02 5.57e+03 7.26e-01 ... (remaining 8248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 10930 1.19 - 2.39: 308 2.39 - 3.58: 72 3.58 - 4.78: 9 4.78 - 5.97: 15 Bond angle restraints: 11334 Sorted by residual: angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 112.29 109.32 2.97 9.40e-01 1.13e+00 1.00e+01 angle pdb=" N VAL B 393 " pdb=" CA VAL B 393 " pdb=" C VAL B 393 " ideal model delta sigma weight residual 112.29 109.34 2.95 9.40e-01 1.13e+00 9.83e+00 angle pdb=" N VAL C 393 " pdb=" CA VAL C 393 " pdb=" C VAL C 393 " ideal model delta sigma weight residual 112.29 109.44 2.85 9.40e-01 1.13e+00 9.22e+00 angle pdb=" C PHE A 212 " pdb=" N THR A 213 " pdb=" CA THR A 213 " ideal model delta sigma weight residual 121.58 116.51 5.07 1.95e+00 2.63e-01 6.75e+00 angle pdb=" C PHE B 212 " pdb=" N THR B 213 " pdb=" CA THR B 213 " ideal model delta sigma weight residual 121.58 116.59 4.99 1.95e+00 2.63e-01 6.55e+00 ... (remaining 11329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.21: 3842 12.21 - 24.41: 581 24.41 - 36.62: 173 36.62 - 48.83: 66 48.83 - 61.03: 27 Dihedral angle restraints: 4689 sinusoidal: 1698 harmonic: 2991 Sorted by residual: dihedral pdb=" CA VAL A 235 " pdb=" C VAL A 235 " pdb=" N PHE A 236 " pdb=" CA PHE A 236 " ideal model delta harmonic sigma weight residual 180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA VAL C 235 " pdb=" C VAL C 235 " pdb=" N PHE C 236 " pdb=" CA PHE C 236 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA VAL B 235 " pdb=" C VAL B 235 " pdb=" N PHE B 236 " pdb=" CA PHE B 236 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 714 0.029 - 0.057: 388 0.057 - 0.085: 172 0.085 - 0.114: 64 0.114 - 0.142: 18 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA PRO C 430 " pdb=" N PRO C 430 " pdb=" C PRO C 430 " pdb=" CB PRO C 430 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA PRO A 430 " pdb=" N PRO A 430 " pdb=" C PRO A 430 " pdb=" CB PRO A 430 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA PRO B 430 " pdb=" N PRO B 430 " pdb=" C PRO B 430 " pdb=" CB PRO B 430 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1353 not shown) Planarity restraints: 1365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 336 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 337 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 336 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO A 337 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 336 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO B 337 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.023 5.00e-02 4.00e+02 ... (remaining 1362 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 142 2.70 - 3.25: 8455 3.25 - 3.80: 14183 3.80 - 4.35: 18509 4.35 - 4.90: 30033 Nonbonded interactions: 71322 Sorted by model distance: nonbonded pdb=" OD1 ASP B 111 " pdb=" NZ LYS B 112 " model vdw 2.152 3.120 nonbonded pdb=" OD1 ASP A 111 " pdb=" NZ LYS A 112 " model vdw 2.154 3.120 nonbonded pdb=" OD1 ASP C 111 " pdb=" NZ LYS C 112 " model vdw 2.155 3.120 nonbonded pdb=" O ASP C 101 " pdb=" NH2 ARG C 124 " model vdw 2.282 3.120 nonbonded pdb=" O ASP A 101 " pdb=" NH2 ARG A 124 " model vdw 2.282 3.120 ... (remaining 71317 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: 0.06 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: 0.010 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.180 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 0.037 8253 Z= 0.299 Angle : 0.534 5.974 11334 Z= 0.292 Chirality : 0.044 0.142 1356 Planarity : 0.005 0.042 1365 Dihedral : 14.678 61.033 2775 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 15.22 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.27), residues: 1029 helix: 1.26 (0.19), residues: 738 sheet: None (None), residues: 0 loop : 0.40 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 108 HIS 0.004 0.001 HIS A 319 PHE 0.016 0.002 PHE B 361 TYR 0.011 0.002 TYR B 348 ARG 0.002 0.000 ARG C 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.959 Fit side-chains REVERT: A 230 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7832 (mttt) REVERT: A 382 MET cc_start: 0.8603 (ttp) cc_final: 0.8381 (ttm) REVERT: B 175 SER cc_start: 0.8674 (t) cc_final: 0.8351 (p) REVERT: B 230 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8149 (mttt) REVERT: C 175 SER cc_start: 0.8658 (t) cc_final: 0.8375 (p) REVERT: C 230 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7770 (mttt) REVERT: C 297 ASP cc_start: 0.8564 (p0) cc_final: 0.8322 (p0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.9132 time to fit residues: 114.6333 Evaluate side-chains 101 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.080080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.064016 restraints weight = 10152.018| |-----------------------------------------------------------------------------| r_work (start): 0.2584 rms_B_bonded: 1.62 r_work: 0.2479 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2373 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8253 Z= 0.260 Angle : 0.504 5.982 11334 Z= 0.263 Chirality : 0.043 0.142 1356 Planarity : 0.005 0.045 1365 Dihedral : 4.332 16.629 1092 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.31 % Allowed : 14.30 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.26), residues: 1029 helix: 1.53 (0.19), residues: 738 sheet: None (None), residues: 0 loop : 0.51 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 108 HIS 0.002 0.001 HIS A 319 PHE 0.015 0.001 PHE A 361 TYR 0.011 0.002 TYR C 348 ARG 0.002 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.897 Fit side-chains REVERT: A 230 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7245 (mttt) REVERT: B 175 SER cc_start: 0.7801 (t) cc_final: 0.7510 (p) REVERT: B 187 MET cc_start: 0.7888 (tpt) cc_final: 0.7677 (tpp) REVERT: B 230 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7572 (mttt) REVERT: C 175 SER cc_start: 0.7641 (t) cc_final: 0.7375 (p) REVERT: C 230 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7160 (mttt) REVERT: C 297 ASP cc_start: 0.8447 (p0) cc_final: 0.8227 (p0) outliers start: 20 outliers final: 4 residues processed: 108 average time/residue: 1.0215 time to fit residues: 118.5083 Evaluate side-chains 98 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 435 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.081265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.065208 restraints weight = 10345.203| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 1.64 r_work: 0.2501 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2395 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8253 Z= 0.203 Angle : 0.470 5.906 11334 Z= 0.243 Chirality : 0.041 0.138 1356 Planarity : 0.005 0.047 1365 Dihedral : 4.196 15.495 1092 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.19 % Allowed : 13.84 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.26), residues: 1029 helix: 1.81 (0.19), residues: 738 sheet: None (None), residues: 0 loop : 0.69 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 366 HIS 0.002 0.001 HIS B 319 PHE 0.012 0.001 PHE C 361 TYR 0.010 0.001 TYR B 429 ARG 0.001 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.821 Fit side-chains REVERT: A 230 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7364 (mttt) REVERT: B 175 SER cc_start: 0.7825 (t) cc_final: 0.7529 (p) REVERT: B 198 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: B 230 LYS cc_start: 0.8375 (mtpt) cc_final: 0.7692 (mttt) REVERT: B 370 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6919 (mp) REVERT: C 175 SER cc_start: 0.7665 (t) cc_final: 0.7407 (p) REVERT: C 230 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7344 (mttt) REVERT: C 297 ASP cc_start: 0.8456 (p0) cc_final: 0.8232 (p0) outliers start: 19 outliers final: 7 residues processed: 107 average time/residue: 0.9309 time to fit residues: 107.7748 Evaluate side-chains 104 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 273 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.081137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.065158 restraints weight = 10341.522| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 1.63 r_work: 0.2501 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2395 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8253 Z= 0.202 Angle : 0.469 5.895 11334 Z= 0.241 Chirality : 0.041 0.138 1356 Planarity : 0.005 0.049 1365 Dihedral : 4.149 15.106 1092 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.54 % Allowed : 13.73 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.26), residues: 1029 helix: 1.84 (0.18), residues: 741 sheet: None (None), residues: 0 loop : 0.92 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 366 HIS 0.002 0.001 HIS A 319 PHE 0.012 0.001 PHE C 361 TYR 0.010 0.001 TYR B 429 ARG 0.001 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.822 Fit side-chains REVERT: A 198 GLU cc_start: 0.8458 (tp30) cc_final: 0.8234 (mm-30) REVERT: A 230 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7445 (mttt) REVERT: B 175 SER cc_start: 0.7851 (t) cc_final: 0.7560 (p) REVERT: B 198 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7862 (tp30) REVERT: B 230 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7553 (mttt) REVERT: B 370 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6924 (mp) REVERT: C 175 SER cc_start: 0.7657 (t) cc_final: 0.7404 (p) REVERT: C 230 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7404 (mttt) REVERT: C 297 ASP cc_start: 0.8456 (p0) cc_final: 0.8237 (p0) outliers start: 22 outliers final: 10 residues processed: 108 average time/residue: 0.8917 time to fit residues: 104.3898 Evaluate side-chains 109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 273 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.082096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.066222 restraints weight = 10184.259| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 1.62 r_work: 0.2519 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8253 Z= 0.176 Angle : 0.459 5.842 11334 Z= 0.235 Chirality : 0.041 0.136 1356 Planarity : 0.004 0.049 1365 Dihedral : 4.072 15.424 1092 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.61 % Allowed : 15.34 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.26), residues: 1029 helix: 1.94 (0.18), residues: 741 sheet: None (None), residues: 0 loop : 0.98 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 366 HIS 0.002 0.000 HIS B 319 PHE 0.011 0.001 PHE C 361 TYR 0.010 0.001 TYR B 429 ARG 0.001 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.811 Fit side-chains REVERT: A 198 GLU cc_start: 0.8458 (tp30) cc_final: 0.8241 (mm-30) REVERT: A 230 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7504 (mttt) REVERT: B 175 SER cc_start: 0.7853 (t) cc_final: 0.7570 (p) REVERT: B 198 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: B 230 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7553 (mttt) REVERT: C 175 SER cc_start: 0.7656 (t) cc_final: 0.7411 (p) REVERT: C 198 GLU cc_start: 0.8486 (tp30) cc_final: 0.8219 (mm-30) REVERT: C 230 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7431 (mttt) REVERT: C 297 ASP cc_start: 0.8463 (p0) cc_final: 0.8236 (p0) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.9260 time to fit residues: 104.2948 Evaluate side-chains 106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 273 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.081865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.065896 restraints weight = 10210.165| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 1.63 r_work: 0.2514 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2409 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8253 Z= 0.191 Angle : 0.468 6.410 11334 Z= 0.238 Chirality : 0.041 0.137 1356 Planarity : 0.004 0.049 1365 Dihedral : 4.063 15.351 1092 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.96 % Allowed : 15.69 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.26), residues: 1029 helix: 1.97 (0.18), residues: 741 sheet: None (None), residues: 0 loop : 1.02 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 108 HIS 0.002 0.000 HIS B 319 PHE 0.011 0.001 PHE C 361 TYR 0.010 0.001 TYR B 429 ARG 0.001 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.870 Fit side-chains REVERT: A 230 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7477 (mttt) REVERT: B 175 SER cc_start: 0.7844 (t) cc_final: 0.7561 (p) REVERT: B 198 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: B 230 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7576 (mttt) REVERT: B 370 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6927 (mp) REVERT: C 175 SER cc_start: 0.7646 (t) cc_final: 0.7401 (p) REVERT: C 198 GLU cc_start: 0.8434 (tp30) cc_final: 0.8187 (mm-30) REVERT: C 230 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7425 (mttt) REVERT: C 297 ASP cc_start: 0.8454 (p0) cc_final: 0.8225 (p0) outliers start: 17 outliers final: 11 residues processed: 104 average time/residue: 0.9179 time to fit residues: 103.2793 Evaluate side-chains 108 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 273 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.081490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.065311 restraints weight = 10172.634| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 1.65 r_work: 0.2499 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8253 Z= 0.193 Angle : 0.472 6.844 11334 Z= 0.240 Chirality : 0.041 0.137 1356 Planarity : 0.004 0.049 1365 Dihedral : 4.055 15.721 1092 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.73 % Allowed : 15.69 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.26), residues: 1029 helix: 2.00 (0.18), residues: 741 sheet: None (None), residues: 0 loop : 1.04 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 108 HIS 0.002 0.001 HIS B 319 PHE 0.011 0.001 PHE B 361 TYR 0.010 0.001 TYR B 429 ARG 0.001 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.950 Fit side-chains REVERT: A 230 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7527 (mttt) REVERT: B 175 SER cc_start: 0.7933 (t) cc_final: 0.7654 (p) REVERT: B 198 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: B 230 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7643 (mttt) REVERT: B 370 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7027 (mp) REVERT: C 175 SER cc_start: 0.7742 (t) cc_final: 0.7499 (p) REVERT: C 198 GLU cc_start: 0.8500 (tp30) cc_final: 0.8245 (mm-30) REVERT: C 230 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7489 (mttt) REVERT: C 297 ASP cc_start: 0.8515 (p0) cc_final: 0.8295 (p0) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 0.9800 time to fit residues: 108.0046 Evaluate side-chains 109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 273 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.081554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.065307 restraints weight = 10252.184| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 1.66 r_work: 0.2499 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8253 Z= 0.194 Angle : 0.475 6.137 11334 Z= 0.241 Chirality : 0.041 0.137 1356 Planarity : 0.004 0.049 1365 Dihedral : 4.041 15.072 1092 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.96 % Allowed : 15.69 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.26), residues: 1029 helix: 2.01 (0.18), residues: 741 sheet: None (None), residues: 0 loop : 1.07 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 108 HIS 0.002 0.001 HIS B 319 PHE 0.012 0.001 PHE B 361 TYR 0.010 0.001 TYR B 429 ARG 0.001 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.828 Fit side-chains REVERT: A 230 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7522 (mttt) REVERT: B 175 SER cc_start: 0.7949 (t) cc_final: 0.7670 (p) REVERT: B 198 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7936 (tp30) REVERT: B 230 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7523 (mttt) REVERT: B 370 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7025 (mp) REVERT: C 175 SER cc_start: 0.7715 (t) cc_final: 0.7477 (p) REVERT: C 198 GLU cc_start: 0.8494 (tp30) cc_final: 0.8247 (mm-30) REVERT: C 230 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7492 (mttt) REVERT: C 297 ASP cc_start: 0.8520 (p0) cc_final: 0.8298 (p0) outliers start: 17 outliers final: 11 residues processed: 102 average time/residue: 0.9200 time to fit residues: 101.5577 Evaluate side-chains 106 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 273 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.0370 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.082764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.066627 restraints weight = 10271.652| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 1.66 r_work: 0.2521 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8253 Z= 0.168 Angle : 0.468 7.105 11334 Z= 0.236 Chirality : 0.040 0.136 1356 Planarity : 0.004 0.049 1365 Dihedral : 3.974 15.492 1092 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.50 % Allowed : 16.15 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.26), residues: 1029 helix: 2.09 (0.18), residues: 741 sheet: None (None), residues: 0 loop : 1.07 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 366 HIS 0.002 0.000 HIS A 319 PHE 0.011 0.001 PHE B 361 TYR 0.010 0.001 TYR B 348 ARG 0.001 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.932 Fit side-chains REVERT: A 230 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7561 (mttt) REVERT: B 175 SER cc_start: 0.7948 (t) cc_final: 0.7671 (p) REVERT: B 198 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: B 230 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7551 (mttt) REVERT: B 370 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7060 (mp) REVERT: C 175 SER cc_start: 0.7699 (t) cc_final: 0.7455 (p) REVERT: C 198 GLU cc_start: 0.8487 (tp30) cc_final: 0.8236 (mm-30) REVERT: C 230 LYS cc_start: 0.8421 (mtpt) cc_final: 0.7732 (mttt) REVERT: C 297 ASP cc_start: 0.8506 (p0) cc_final: 0.8305 (p0) outliers start: 13 outliers final: 10 residues processed: 102 average time/residue: 0.9168 time to fit residues: 101.2382 Evaluate side-chains 108 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 chunk 98 optimal weight: 1.9990 chunk 78 optimal weight: 0.0030 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.0010 chunk 68 optimal weight: 10.0000 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.085029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.068896 restraints weight = 10190.593| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 1.69 r_work: 0.2563 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8253 Z= 0.139 Angle : 0.455 9.207 11334 Z= 0.229 Chirality : 0.040 0.143 1356 Planarity : 0.004 0.048 1365 Dihedral : 3.850 14.909 1092 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.50 % Allowed : 16.15 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.26), residues: 1029 helix: 2.25 (0.18), residues: 741 sheet: None (None), residues: 0 loop : 1.04 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 366 HIS 0.001 0.000 HIS B 319 PHE 0.010 0.001 PHE B 361 TYR 0.010 0.001 TYR B 348 ARG 0.001 0.000 ARG A 434 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.893 Fit side-chains REVERT: A 230 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7542 (mttt) REVERT: B 175 SER cc_start: 0.7882 (t) cc_final: 0.7614 (p) REVERT: B 198 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7878 (tp30) REVERT: B 230 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7515 (mttt) REVERT: C 175 SER cc_start: 0.7668 (t) cc_final: 0.7435 (p) REVERT: C 198 GLU cc_start: 0.8447 (tp30) cc_final: 0.8197 (mm-30) REVERT: C 230 LYS cc_start: 0.8411 (mtpt) cc_final: 0.7723 (mttt) REVERT: C 399 THR cc_start: 0.7488 (p) cc_final: 0.7246 (p) outliers start: 13 outliers final: 8 residues processed: 112 average time/residue: 0.8808 time to fit residues: 107.1707 Evaluate side-chains 109 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 85 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.084012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.067940 restraints weight = 10247.840| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 1.66 r_work: 0.2547 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.003 0.032 8253 Z= 0.159 Angle : 0.473 9.039 11334 Z= 0.238 Chirality : 0.040 0.137 1356 Planarity : 0.004 0.049 1365 Dihedral : 3.870 15.011 1092 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.27 % Allowed : 16.84 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.26), residues: 1029 helix: 2.27 (0.18), residues: 741 sheet: None (None), residues: 0 loop : 1.10 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 108 HIS 0.002 0.000 HIS B 319 PHE 0.011 0.001 PHE B 361 TYR 0.009 0.001 TYR C 348 ARG 0.001 0.000 ARG B 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5340.57 seconds wall clock time: 91 minutes 52.17 seconds (5512.17 seconds total)