Starting phenix.real_space_refine on Wed Mar 5 15:46:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tjo_10512/03_2025/6tjo_10512.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tjo_10512/03_2025/6tjo_10512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tjo_10512/03_2025/6tjo_10512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tjo_10512/03_2025/6tjo_10512.map" model { file = "/net/cci-nas-00/data/ceres_data/6tjo_10512/03_2025/6tjo_10512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tjo_10512/03_2025/6tjo_10512.cif" } resolution = 3.2 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= 0.003 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 6 5.16 5 C 1521 2.51 5 N 453 2.21 5 O 459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2439 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Restraints were copied for chains: C, B Time building chain proxies: 2.03, per 1000 atoms: 0.83 Number of scatterers: 2439 At special positions: 0 Unit cell: (105.8, 81.65, 34.5, 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 6 16.00 O 459 8.00 N 453 7.00 C 1521 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: 0.50 Conformation dependent library (CDL) restraints added in 248.8 milliseconds 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 286 through 287 removed outlier: 6.326A pdb=" N ASN A 286 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.291A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 327 through 328 removed outlier: 6.487A pdb=" N ASN A 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.454A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 350 through 351 removed outlier: 5.840A pdb=" N VAL B 350 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.717A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) 10 hydrogen bonds defined for protein. 30 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: 0.40 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 672 1.33 - 1.44: 302 1.44 - 1.55: 1492 1.55 - 1.67: 0 1.67 - 1.78: 6 Bond restraints: 2472 Sorted by residual: bond pdb=" CD LYS A 311 " pdb=" CE LYS A 311 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CD LYS C 311 " pdb=" CE LYS C 311 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.87e+00 bond pdb=" CD LYS B 311 " pdb=" CE LYS B 311 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.81e+00 bond pdb=" C LYS C 280 " pdb=" N LYS C 281 " ideal model delta sigma weight residual 1.329 1.291 0.038 1.79e-02 3.12e+03 4.39e+00 bond pdb=" C LYS B 280 " pdb=" N LYS B 281 " ideal model delta sigma weight residual 1.329 1.292 0.037 1.79e-02 3.12e+03 4.33e+00 ... (remaining 2467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 3010 1.82 - 3.65: 246 3.65 - 5.47: 20 5.47 - 7.30: 21 7.30 - 9.12: 6 Bond angle restraints: 3303 Sorted by residual: angle pdb=" N SER C 324 " pdb=" CA SER C 324 " pdb=" C SER C 324 " ideal model delta sigma weight residual 110.80 117.73 -6.93 2.13e+00 2.20e-01 1.06e+01 angle pdb=" N SER A 324 " pdb=" CA SER A 324 " pdb=" C SER A 324 " ideal model delta sigma weight residual 110.80 117.72 -6.92 2.13e+00 2.20e-01 1.06e+01 angle pdb=" N SER B 324 " pdb=" CA SER B 324 " pdb=" C SER B 324 " ideal model delta sigma weight residual 110.80 117.71 -6.91 2.13e+00 2.20e-01 1.05e+01 angle pdb=" C LYS A 280 " pdb=" N LYS A 281 " pdb=" CA LYS A 281 " ideal model delta sigma weight residual 122.58 116.18 6.40 2.07e+00 2.33e-01 9.55e+00 angle pdb=" C LYS B 280 " pdb=" N LYS B 281 " pdb=" CA LYS B 281 " ideal model delta sigma weight residual 122.58 116.22 6.36 2.07e+00 2.33e-01 9.45e+00 ... (remaining 3298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.22: 1225 8.22 - 16.44: 218 16.44 - 24.65: 60 24.65 - 32.87: 15 32.87 - 41.09: 9 Dihedral angle restraints: 1527 sinusoidal: 642 harmonic: 885 Sorted by residual: dihedral pdb=" CA GLY B 323 " pdb=" C GLY B 323 " pdb=" N SER B 324 " pdb=" CA SER B 324 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLY A 323 " pdb=" C GLY A 323 " pdb=" N SER A 324 " pdb=" CA SER A 324 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLY C 323 " pdb=" C GLY C 323 " pdb=" N SER C 324 " pdb=" CA SER C 324 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 1524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 247 0.069 - 0.138: 113 0.138 - 0.206: 6 0.206 - 0.275: 3 0.275 - 0.344: 3 Chirality restraints: 372 Sorted by residual: chirality pdb=" CB ILE A 360 " pdb=" CA ILE A 360 " pdb=" CG1 ILE A 360 " pdb=" CG2 ILE A 360 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB ILE B 360 " pdb=" CA ILE B 360 " pdb=" CG1 ILE B 360 " pdb=" CG2 ILE B 360 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB ILE C 360 " pdb=" CA ILE C 360 " pdb=" CG1 ILE C 360 " pdb=" CG2 ILE C 360 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 369 not shown) Planarity restraints: 423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 300 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO C 301 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 301 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 301 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 300 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO A 301 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 300 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO B 301 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " -0.034 5.00e-02 4.00e+02 ... (remaining 420 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 900 2.90 - 3.40: 2046 3.40 - 3.90: 3884 3.90 - 4.40: 4038 4.40 - 4.90: 8082 Nonbonded interactions: 18950 Sorted by model distance: nonbonded pdb=" N ASP A 295 " pdb=" OD1 ASP A 295 " model vdw 2.394 3.120 nonbonded pdb=" N ASP C 295 " pdb=" OD1 ASP C 295 " model vdw 2.394 3.120 nonbonded pdb=" N ASP B 295 " pdb=" OD1 ASP B 295 " model vdw 2.395 3.120 nonbonded pdb=" OD1 ASP B 314 " pdb=" N LEU B 315 " model vdw 2.525 3.120 nonbonded pdb=" OD1 ASP C 314 " pdb=" N LEU C 315 " model vdw 2.525 3.120 ... (remaining 18945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.930 Find NCS groups from input model: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.013 0.097 2472 Z= 0.833 Angle : 1.182 9.123 3303 Z= 0.614 Chirality : 0.073 0.344 372 Planarity : 0.010 0.063 423 Dihedral : 9.665 41.087 963 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % 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: -4.63 (0.32), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.25), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS A 329 PHE 0.010 0.003 PHE B 378 TYR 0.011 0.005 TYR C 310 ARG 0.004 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.247 Fit side-chains REVERT: A 276 GLN cc_start: 0.7459 (mt0) cc_final: 0.6638 (mp10) REVERT: A 295 ASP cc_start: 0.8802 (p0) cc_final: 0.8561 (p0) REVERT: A 321 LYS cc_start: 0.7724 (mttt) cc_final: 0.7138 (tmtt) REVERT: A 343 LYS cc_start: 0.8056 (mttt) cc_final: 0.7740 (mtpt) REVERT: A 372 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7334 (mp0) REVERT: A 379 ARG cc_start: 0.6702 (mtt180) cc_final: 0.6394 (mtp180) REVERT: B 276 GLN cc_start: 0.8224 (mt0) cc_final: 0.7371 (mp10) REVERT: B 343 LYS cc_start: 0.8649 (mttt) cc_final: 0.8443 (ttmm) REVERT: B 372 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7450 (mp0) REVERT: C 276 GLN cc_start: 0.7050 (mt0) cc_final: 0.6234 (mp10) REVERT: C 291 CYS cc_start: 0.8744 (t) cc_final: 0.8002 (p) REVERT: C 295 ASP cc_start: 0.8976 (p0) cc_final: 0.8766 (p0) REVERT: C 343 LYS cc_start: 0.8369 (mttt) cc_final: 0.8150 (mtpt) REVERT: C 379 ARG cc_start: 0.6405 (mtt180) cc_final: 0.6059 (mtp180) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1467 time to fit residues: 8.7825 Evaluate side-chains 45 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 362 HIS C 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.114126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.094178 restraints weight = 3611.770| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.12 r_work: 0.3808 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2472 Z= 0.286 Angle : 0.676 6.101 3303 Z= 0.349 Chirality : 0.052 0.134 372 Planarity : 0.005 0.038 423 Dihedral : 6.479 25.396 327 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.48 % Allowed : 7.45 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.007 0.001 PHE A 378 TYR 0.018 0.004 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8861 (p0) cc_final: 0.8644 (p0) REVERT: A 321 LYS cc_start: 0.7911 (mttt) cc_final: 0.7281 (tmtt) REVERT: A 343 LYS cc_start: 0.8437 (mttt) cc_final: 0.8144 (mtpt) REVERT: A 372 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7611 (mp0) REVERT: B 295 ASP cc_start: 0.8761 (p0) cc_final: 0.8117 (p0) REVERT: B 348 ASP cc_start: 0.8558 (m-30) cc_final: 0.7107 (p0) REVERT: B 358 ASP cc_start: 0.7882 (t0) cc_final: 0.7604 (t0) REVERT: B 372 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7720 (mp0) REVERT: C 295 ASP cc_start: 0.8637 (p0) cc_final: 0.8415 (p0) REVERT: C 310 TYR cc_start: 0.9109 (t80) cc_final: 0.8848 (t80) REVERT: C 321 LYS cc_start: 0.8000 (mttt) cc_final: 0.7199 (tptp) REVERT: C 348 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8039 (t0) REVERT: C 349 ARG cc_start: 0.7477 (mtp180) cc_final: 0.6301 (mmm160) REVERT: C 379 ARG cc_start: 0.7035 (mtt180) cc_final: 0.6711 (mmm-85) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 0.1949 time to fit residues: 12.0540 Evaluate side-chains 53 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.095266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.074484 restraints weight = 3953.749| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.18 r_work: 0.3555 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2472 Z= 0.373 Angle : 0.744 6.688 3303 Z= 0.375 Chirality : 0.054 0.180 372 Planarity : 0.004 0.030 423 Dihedral : 6.543 24.915 327 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 3.90 % Allowed : 9.57 % Favored : 86.52 % 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: -3.79 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 329 PHE 0.007 0.001 PHE B 378 TYR 0.023 0.003 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.310 Fit side-chains REVERT: A 291 CYS cc_start: 0.8934 (p) cc_final: 0.7969 (p) REVERT: A 321 LYS cc_start: 0.7448 (mttt) cc_final: 0.6810 (tmtt) REVERT: A 343 LYS cc_start: 0.8141 (mttt) cc_final: 0.7799 (mtpt) REVERT: A 348 ASP cc_start: 0.8000 (t0) cc_final: 0.7749 (t0) REVERT: A 372 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7587 (mp0) REVERT: B 276 GLN cc_start: 0.8135 (mt0) cc_final: 0.7320 (mp10) REVERT: B 291 CYS cc_start: 0.8139 (p) cc_final: 0.7893 (m) REVERT: B 295 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7909 (p0) REVERT: B 338 GLU cc_start: 0.8379 (mp0) cc_final: 0.8075 (mp0) REVERT: B 358 ASP cc_start: 0.8066 (t0) cc_final: 0.7815 (t0) REVERT: B 372 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7445 (mp0) REVERT: C 276 GLN cc_start: 0.7276 (mt0) cc_final: 0.6620 (mp10) REVERT: C 321 LYS cc_start: 0.7455 (mttt) cc_final: 0.6645 (tptp) REVERT: C 336 GLN cc_start: 0.7801 (mt0) cc_final: 0.7541 (mt0) REVERT: C 338 GLU cc_start: 0.7452 (mp0) cc_final: 0.7129 (mp0) REVERT: C 349 ARG cc_start: 0.7246 (mtp180) cc_final: 0.6174 (mmm160) REVERT: C 379 ARG cc_start: 0.6835 (mtt180) cc_final: 0.6503 (mmm-85) outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.1760 time to fit residues: 10.8773 Evaluate side-chains 55 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 343 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.094860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.073829 restraints weight = 3963.902| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.20 r_work: 0.3556 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 2472 Z= 0.376 Angle : 0.759 10.045 3303 Z= 0.377 Chirality : 0.053 0.166 372 Planarity : 0.003 0.026 423 Dihedral : 6.524 25.100 327 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 4.61 % Allowed : 8.87 % Favored : 86.52 % 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: -3.55 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.007 0.001 PHE B 378 TYR 0.025 0.004 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.299 Fit side-chains REVERT: A 321 LYS cc_start: 0.7479 (mttt) cc_final: 0.6856 (tmtt) REVERT: A 343 LYS cc_start: 0.8208 (mttt) cc_final: 0.7847 (mtpt) REVERT: A 348 ASP cc_start: 0.8139 (t0) cc_final: 0.7922 (t0) REVERT: A 372 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7480 (mp0) REVERT: B 285 SER cc_start: 0.9253 (p) cc_final: 0.9050 (p) REVERT: B 291 CYS cc_start: 0.8152 (p) cc_final: 0.7905 (m) REVERT: B 295 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7864 (p0) REVERT: B 325 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7814 (mp) REVERT: B 358 ASP cc_start: 0.7970 (t0) cc_final: 0.7590 (t0) REVERT: B 372 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7438 (mp0) REVERT: C 276 GLN cc_start: 0.7328 (mt0) cc_final: 0.6671 (mp10) REVERT: C 321 LYS cc_start: 0.7531 (mttt) cc_final: 0.6673 (tmtt) REVERT: C 338 GLU cc_start: 0.7512 (mp0) cc_final: 0.7274 (mp0) REVERT: C 348 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8007 (t0) REVERT: C 349 ARG cc_start: 0.7294 (mtp180) cc_final: 0.6051 (mmm160) REVERT: C 379 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6536 (mmm-85) outliers start: 13 outliers final: 9 residues processed: 48 average time/residue: 0.1781 time to fit residues: 9.9523 Evaluate side-chains 56 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.099695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.078067 restraints weight = 3850.537| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.29 r_work: 0.3633 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2472 Z= 0.217 Angle : 0.699 10.873 3303 Z= 0.337 Chirality : 0.051 0.152 372 Planarity : 0.003 0.020 423 Dihedral : 5.975 24.272 327 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.61 % Allowed : 9.22 % Favored : 86.17 % 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: -3.36 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.005 0.001 PHE C 378 TYR 0.024 0.003 TYR B 310 ARG 0.000 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7417 (mttt) cc_final: 0.6893 (tmtt) REVERT: A 343 LYS cc_start: 0.8153 (mttt) cc_final: 0.7786 (mtpt) REVERT: A 348 ASP cc_start: 0.8097 (t0) cc_final: 0.7853 (t0) REVERT: A 372 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7452 (mp0) REVERT: A 376 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7873 (tt) REVERT: B 285 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8962 (p) REVERT: B 295 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7987 (p0) REVERT: B 338 GLU cc_start: 0.8370 (mp0) cc_final: 0.8093 (mp0) REVERT: B 358 ASP cc_start: 0.7839 (t0) cc_final: 0.7529 (t0) REVERT: B 372 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7381 (mp0) REVERT: C 276 GLN cc_start: 0.7172 (mt0) cc_final: 0.6490 (mp10) REVERT: C 321 LYS cc_start: 0.7300 (mttt) cc_final: 0.6469 (tptm) REVERT: C 338 GLU cc_start: 0.7537 (mp0) cc_final: 0.7255 (mp0) REVERT: C 348 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8002 (t0) REVERT: C 349 ARG cc_start: 0.7202 (mtp180) cc_final: 0.6012 (mmm160) REVERT: C 379 ARG cc_start: 0.6738 (mtt180) cc_final: 0.6360 (mmm-85) outliers start: 13 outliers final: 4 residues processed: 46 average time/residue: 0.1906 time to fit residues: 10.1796 Evaluate side-chains 48 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.112514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.092578 restraints weight = 3721.858| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.16 r_work: 0.3812 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2472 Z= 0.268 Angle : 0.730 14.228 3303 Z= 0.346 Chirality : 0.052 0.169 372 Planarity : 0.003 0.021 423 Dihedral : 6.061 24.414 327 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 4.61 % Allowed : 8.87 % Favored : 86.52 % 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: -3.36 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.006 0.001 PHE B 378 TYR 0.025 0.003 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.296 Fit side-chains REVERT: A 321 LYS cc_start: 0.7850 (mttt) cc_final: 0.7354 (tmtt) REVERT: A 343 LYS cc_start: 0.8557 (mttt) cc_final: 0.8255 (mtpt) REVERT: A 348 ASP cc_start: 0.8508 (t0) cc_final: 0.8240 (t0) REVERT: A 372 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7744 (mp0) REVERT: B 295 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7854 (p0) REVERT: B 325 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6457 (pt) REVERT: B 358 ASP cc_start: 0.8028 (t0) cc_final: 0.7748 (t0) REVERT: B 372 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7715 (mp0) REVERT: C 276 GLN cc_start: 0.7596 (mt0) cc_final: 0.7051 (mp10) REVERT: C 321 LYS cc_start: 0.7914 (mttt) cc_final: 0.7134 (tptm) REVERT: C 338 GLU cc_start: 0.7782 (mp0) cc_final: 0.7581 (mp0) REVERT: C 348 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8334 (t0) REVERT: C 349 ARG cc_start: 0.7538 (mtp180) cc_final: 0.6299 (mmm160) REVERT: C 379 ARG cc_start: 0.7095 (mtt180) cc_final: 0.6735 (mmm-85) outliers start: 13 outliers final: 5 residues processed: 42 average time/residue: 0.1801 time to fit residues: 8.9075 Evaluate side-chains 44 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.111778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.091489 restraints weight = 3821.612| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.20 r_work: 0.3791 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2472 Z= 0.291 Angle : 0.756 14.364 3303 Z= 0.357 Chirality : 0.052 0.161 372 Planarity : 0.003 0.020 423 Dihedral : 6.102 24.073 327 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.84 % Allowed : 9.57 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.006 0.001 PHE A 378 TYR 0.025 0.003 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.303 Fit side-chains REVERT: A 321 LYS cc_start: 0.7821 (mttt) cc_final: 0.7325 (tmtt) REVERT: A 343 LYS cc_start: 0.8562 (mttt) cc_final: 0.8271 (mtpt) REVERT: A 348 ASP cc_start: 0.8543 (t0) cc_final: 0.8278 (t0) REVERT: A 358 ASP cc_start: 0.7663 (t0) cc_final: 0.7456 (t0) REVERT: A 372 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7729 (mp0) REVERT: B 295 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7844 (p0) REVERT: B 325 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6419 (pt) REVERT: B 358 ASP cc_start: 0.8053 (t0) cc_final: 0.7836 (t0) REVERT: B 372 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7680 (mp0) REVERT: C 276 GLN cc_start: 0.7694 (mt0) cc_final: 0.7095 (mp10) REVERT: C 321 LYS cc_start: 0.7823 (mttt) cc_final: 0.7089 (tmtt) REVERT: C 338 GLU cc_start: 0.7803 (mp0) cc_final: 0.7600 (mp0) REVERT: C 348 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8519 (t0) REVERT: C 349 ARG cc_start: 0.7483 (mtp180) cc_final: 0.6174 (mmm160) REVERT: C 379 ARG cc_start: 0.7139 (mtt180) cc_final: 0.6744 (mmm-85) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.2029 time to fit residues: 9.4597 Evaluate side-chains 44 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 overall best weight: 1.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.232154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.195655 restraints weight = 3014.091| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.45 r_work: 0.4112 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2472 Z= 0.178 Angle : 0.714 13.783 3303 Z= 0.329 Chirality : 0.051 0.160 372 Planarity : 0.003 0.023 423 Dihedral : 5.639 23.631 327 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.84 % Allowed : 10.28 % Favored : 86.88 % 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: -3.26 (0.40), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.004 0.001 PHE A 378 TYR 0.023 0.003 TYR B 310 ARG 0.000 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7869 (mttt) cc_final: 0.7360 (tmtt) REVERT: A 343 LYS cc_start: 0.8607 (mttt) cc_final: 0.8369 (mtpt) REVERT: A 348 ASP cc_start: 0.8665 (t0) cc_final: 0.8455 (t0) REVERT: B 295 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7714 (p0) REVERT: B 298 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8452 (mttt) REVERT: C 276 GLN cc_start: 0.7647 (mt0) cc_final: 0.7141 (mp10) REVERT: C 321 LYS cc_start: 0.7926 (mttt) cc_final: 0.7223 (tmtt) REVERT: C 348 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8541 (t0) REVERT: C 349 ARG cc_start: 0.7569 (mtp180) cc_final: 0.6291 (mmm160) REVERT: C 379 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6906 (mmm-85) outliers start: 8 outliers final: 3 residues processed: 44 average time/residue: 0.1971 time to fit residues: 9.9934 Evaluate side-chains 43 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 9 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.4764 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.107155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.086357 restraints weight = 3824.961| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.25 r_work: 0.3762 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2472 Z= 0.225 Angle : 0.695 10.025 3303 Z= 0.334 Chirality : 0.051 0.177 372 Planarity : 0.003 0.023 423 Dihedral : 5.766 23.451 327 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.77 % Allowed : 12.06 % Favored : 86.17 % 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: -3.25 (0.40), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.004 0.001 PHE A 378 TYR 0.024 0.003 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.301 Fit side-chains REVERT: A 321 LYS cc_start: 0.7660 (mttt) cc_final: 0.7083 (tmtt) REVERT: A 343 LYS cc_start: 0.8497 (mttt) cc_final: 0.8174 (mtpt) REVERT: A 348 ASP cc_start: 0.8485 (t0) cc_final: 0.8251 (t0) REVERT: B 295 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7735 (p0) REVERT: B 298 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8465 (mttt) REVERT: B 358 ASP cc_start: 0.7926 (t0) cc_final: 0.7688 (t0) REVERT: C 276 GLN cc_start: 0.7628 (mt0) cc_final: 0.6975 (mp10) REVERT: C 321 LYS cc_start: 0.7664 (mttt) cc_final: 0.6831 (tmtt) REVERT: C 336 GLN cc_start: 0.8017 (mt0) cc_final: 0.7269 (tt0) REVERT: C 348 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8439 (t0) REVERT: C 349 ARG cc_start: 0.7416 (mtp180) cc_final: 0.6094 (mmm160) REVERT: C 379 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6684 (mmm-85) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.2003 time to fit residues: 9.4974 Evaluate side-chains 44 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 0.0670 overall best weight: 2.4124 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.107020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.087267 restraints weight = 3828.395| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.03 r_work: 0.3582 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2472 Z= 0.322 Angle : 0.743 10.439 3303 Z= 0.362 Chirality : 0.051 0.173 372 Planarity : 0.003 0.021 423 Dihedral : 6.113 24.169 327 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.77 % Allowed : 12.06 % Favored : 86.17 % 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: -3.39 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.005 0.001 PHE B 378 TYR 0.029 0.004 TYR B 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.299 Fit side-chains REVERT: A 321 LYS cc_start: 0.7615 (mttt) cc_final: 0.7087 (tmtt) REVERT: A 343 LYS cc_start: 0.8413 (mttt) cc_final: 0.8088 (mtpt) REVERT: A 348 ASP cc_start: 0.8445 (t0) cc_final: 0.8237 (t0) REVERT: B 295 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7772 (p0) REVERT: C 276 GLN cc_start: 0.7508 (mt0) cc_final: 0.6876 (mp10) REVERT: C 348 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8441 (t0) REVERT: C 349 ARG cc_start: 0.7417 (mtp180) cc_final: 0.6069 (mmm160) REVERT: C 379 ARG cc_start: 0.7074 (mtt180) cc_final: 0.6654 (mmm-85) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.1993 time to fit residues: 8.9170 Evaluate side-chains 39 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.116678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.096330 restraints weight = 3629.215| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 3.13 r_work: 0.3872 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2472 Z= 0.190 Angle : 0.698 9.900 3303 Z= 0.338 Chirality : 0.051 0.217 372 Planarity : 0.003 0.024 423 Dihedral : 5.508 23.802 327 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.13 % Allowed : 12.77 % Favored : 85.11 % 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: -3.25 (0.40), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.003 0.001 PHE A 378 TYR 0.025 0.004 TYR B 310 ARG 0.000 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.32 seconds wall clock time: 31 minutes 45.32 seconds (1905.32 seconds total)