Starting phenix.real_space_refine on Sun Mar 10 14:52:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/03_2024/6tjo_10512.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/03_2024/6tjo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/03_2024/6tjo_10512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/03_2024/6tjo_10512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/03_2024/6tjo_10512.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tjo_10512/03_2024/6tjo_10512.pdb" } 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 Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2439 Number of models: 1 Model: "" Number of chains: 3 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} Chain: "B" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 1.93, per 1000 atoms: 0.79 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 - 3.50 Amino acid : False - 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: 0.91 Conformation dependent library (CDL) restraints added in 428.5 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: 0.24 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: 0.46 Time building geometry restraints manager: 1.00 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: 102.71 - 108.41: 239 108.41 - 114.12: 1357 114.12 - 119.82: 585 119.82 - 125.53: 1093 125.53 - 131.23: 29 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 2.520 nonbonded pdb=" N ASP C 295 " pdb=" OD1 ASP C 295 " model vdw 2.394 2.520 nonbonded pdb=" N ASP B 295 " pdb=" OD1 ASP B 295 " model vdw 2.395 2.520 nonbonded pdb=" OD1 ASP B 314 " pdb=" N LEU B 315 " model vdw 2.525 2.520 nonbonded pdb=" OD1 ASP C 314 " pdb=" N LEU C 315 " model vdw 2.525 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.470 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: 7.020 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.880 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.320 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.313 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: 0.1635 time to fit residues: 9.8117 Evaluate side-chains 45 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1697 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= 0.244 Angle : 0.644 6.076 3303 Z= 0.328 Chirality : 0.052 0.130 372 Planarity : 0.005 0.037 423 Dihedral : 6.317 25.827 327 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.48 % Allowed : 8.16 % Favored : 89.36 % 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: -4.10 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.006 0.001 PHE A 378 TYR 0.018 0.004 TYR B 310 ARG 0.001 0.000 ARG A 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 60 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7435 (mttt) cc_final: 0.6779 (tmtt) REVERT: A 343 LYS cc_start: 0.8160 (mttt) cc_final: 0.7830 (mtpt) REVERT: A 372 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7214 (mp0) REVERT: B 276 GLN cc_start: 0.8241 (mt0) cc_final: 0.7315 (mp10) REVERT: B 295 ASP cc_start: 0.8725 (p0) cc_final: 0.8057 (p0) REVERT: B 348 ASP cc_start: 0.8398 (m-30) cc_final: 0.6965 (p0) REVERT: B 358 ASP cc_start: 0.7863 (t0) cc_final: 0.7576 (t0) REVERT: B 372 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7355 (mp0) REVERT: C 321 LYS cc_start: 0.7491 (mttt) cc_final: 0.6646 (tptp) REVERT: C 343 LYS cc_start: 0.8440 (mttt) cc_final: 0.8214 (mtpt) REVERT: C 348 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7747 (t0) REVERT: C 349 ARG cc_start: 0.7021 (mtp180) cc_final: 0.6023 (mmm160) REVERT: C 356 SER cc_start: 0.8412 (t) cc_final: 0.8205 (p) REVERT: C 379 ARG cc_start: 0.6490 (mtt180) cc_final: 0.6262 (mmm-85) outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 0.1938 time to fit residues: 12.2076 Evaluate side-chains 52 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.0030 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2472 Z= 0.267 Angle : 0.680 6.460 3303 Z= 0.338 Chirality : 0.052 0.148 372 Planarity : 0.004 0.026 423 Dihedral : 6.175 25.403 327 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.26 % Allowed : 7.80 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.37), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.28), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.006 0.001 PHE C 378 TYR 0.018 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 fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7408 (mttt) cc_final: 0.6771 (tmtt) REVERT: A 343 LYS cc_start: 0.8191 (mttt) cc_final: 0.7849 (mtpt) REVERT: A 358 ASP cc_start: 0.7624 (t0) cc_final: 0.7400 (t0) REVERT: A 372 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7293 (mp0) REVERT: B 276 GLN cc_start: 0.8178 (mt0) cc_final: 0.7278 (mp10) REVERT: B 295 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7836 (p0) REVERT: B 325 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7783 (mp) REVERT: B 338 GLU cc_start: 0.8105 (mp0) cc_final: 0.7761 (mp0) REVERT: B 348 ASP cc_start: 0.8448 (m-30) cc_final: 0.6937 (p0) REVERT: B 358 ASP cc_start: 0.8097 (t0) cc_final: 0.7893 (t0) REVERT: B 372 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7283 (mp0) REVERT: C 276 GLN cc_start: 0.7192 (mt0) cc_final: 0.6499 (mp10) REVERT: C 321 LYS cc_start: 0.7446 (mttt) cc_final: 0.6702 (tmtt) REVERT: C 343 LYS cc_start: 0.8467 (mttt) cc_final: 0.8238 (mtpt) REVERT: C 349 ARG cc_start: 0.7041 (mtp180) cc_final: 0.6067 (mmm160) REVERT: C 356 SER cc_start: 0.8332 (t) cc_final: 0.8116 (p) REVERT: C 379 ARG cc_start: 0.6578 (mtt180) cc_final: 0.6331 (mmm-85) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.1778 time to fit residues: 10.7465 Evaluate side-chains 56 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 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 305 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2429 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= 0.371 Angle : 0.723 6.525 3303 Z= 0.365 Chirality : 0.053 0.146 372 Planarity : 0.004 0.025 423 Dihedral : 6.450 25.805 327 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 5.32 % Allowed : 7.09 % 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: -3.67 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 329 PHE 0.007 0.001 PHE A 378 TYR 0.021 0.003 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 64 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.317 Fit side-chains REVERT: A 295 ASP cc_start: 0.8620 (p0) cc_final: 0.8075 (p0) REVERT: A 321 LYS cc_start: 0.7289 (mttt) cc_final: 0.6664 (tmtt) REVERT: A 343 LYS cc_start: 0.8215 (mttt) cc_final: 0.7858 (mtpt) REVERT: A 372 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7382 (mp0) REVERT: B 276 GLN cc_start: 0.8148 (mt0) cc_final: 0.7273 (mp10) REVERT: B 285 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8968 (p) REVERT: B 295 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7851 (p0) REVERT: B 325 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7838 (mp) REVERT: B 348 ASP cc_start: 0.8497 (m-30) cc_final: 0.6992 (p0) REVERT: B 358 ASP cc_start: 0.8078 (t0) cc_final: 0.7666 (t0) REVERT: B 372 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7253 (mp0) REVERT: C 276 GLN cc_start: 0.7181 (mt0) cc_final: 0.6482 (mp10) REVERT: C 298 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8560 (mtmm) REVERT: C 321 LYS cc_start: 0.7440 (mttt) cc_final: 0.6706 (tmtt) REVERT: C 336 GLN cc_start: 0.7849 (mt0) cc_final: 0.7588 (mt0) REVERT: C 338 GLU cc_start: 0.7320 (mp0) cc_final: 0.7053 (mp0) REVERT: C 343 LYS cc_start: 0.8451 (mttt) cc_final: 0.8215 (mtpt) REVERT: C 348 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7869 (t0) REVERT: C 349 ARG cc_start: 0.7055 (mtp180) cc_final: 0.5923 (mmm160) REVERT: C 379 ARG cc_start: 0.6742 (mtt180) cc_final: 0.6383 (mmm-85) outliers start: 15 outliers final: 8 residues processed: 53 average time/residue: 0.1855 time to fit residues: 11.4018 Evaluate side-chains 60 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 285 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 359 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2472 Z= 0.329 Angle : 0.699 6.457 3303 Z= 0.350 Chirality : 0.052 0.140 372 Planarity : 0.003 0.022 423 Dihedral : 6.286 25.502 327 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.96 % Allowed : 7.45 % 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: -3.55 (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 0.017 0.003 TYR B 310 ARG 0.001 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 62 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.321 Fit side-chains REVERT: A 295 ASP cc_start: 0.8530 (p0) cc_final: 0.8011 (p0) REVERT: A 321 LYS cc_start: 0.7263 (mttt) cc_final: 0.6686 (tmtt) REVERT: A 343 LYS cc_start: 0.8261 (mttt) cc_final: 0.7883 (mtpt) REVERT: A 358 ASP cc_start: 0.7573 (t0) cc_final: 0.7298 (t0) REVERT: A 372 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7261 (mp0) REVERT: A 376 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7819 (tt) REVERT: B 285 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 295 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7842 (p0) REVERT: B 325 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7864 (mp) REVERT: B 338 GLU cc_start: 0.8145 (mp0) cc_final: 0.7847 (mp0) REVERT: B 358 ASP cc_start: 0.8071 (t0) cc_final: 0.7639 (t0) REVERT: B 372 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7216 (mp0) REVERT: C 276 GLN cc_start: 0.7205 (mt0) cc_final: 0.6505 (mp10) REVERT: C 298 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8452 (mtmm) REVERT: C 321 LYS cc_start: 0.7322 (mttt) cc_final: 0.6556 (tmtt) REVERT: C 343 LYS cc_start: 0.8443 (mttt) cc_final: 0.8233 (mtpt) REVERT: C 348 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8020 (t0) REVERT: C 349 ARG cc_start: 0.7063 (mtp180) cc_final: 0.5963 (mmm160) REVERT: C 379 ARG cc_start: 0.6744 (mtt180) cc_final: 0.6366 (mmm-85) outliers start: 14 outliers final: 8 residues processed: 51 average time/residue: 0.1817 time to fit residues: 10.7203 Evaluate side-chains 60 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 305 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 359 ASN 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 7 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2472 Z= 0.347 Angle : 0.702 6.454 3303 Z= 0.352 Chirality : 0.052 0.140 372 Planarity : 0.003 0.022 423 Dihedral : 6.312 25.474 327 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 5.32 % Allowed : 7.09 % 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: -3.62 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.005 0.001 PHE A 378 TYR 0.014 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 63 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.304 Fit side-chains REVERT: A 295 ASP cc_start: 0.8453 (p0) cc_final: 0.7761 (p0) REVERT: A 321 LYS cc_start: 0.7243 (mttt) cc_final: 0.6701 (tmtt) REVERT: A 343 LYS cc_start: 0.8282 (mttt) cc_final: 0.7919 (mtpt) REVERT: A 372 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7267 (mp0) REVERT: A 376 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7869 (tt) REVERT: B 285 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8878 (p) REVERT: B 295 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7821 (p0) REVERT: B 325 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7829 (mp) REVERT: B 338 GLU cc_start: 0.8123 (mp0) cc_final: 0.7806 (mp0) REVERT: B 358 ASP cc_start: 0.8040 (t0) cc_final: 0.7624 (t0) REVERT: B 372 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7262 (mp0) REVERT: C 276 GLN cc_start: 0.7247 (mt0) cc_final: 0.6536 (mp10) REVERT: C 295 ASP cc_start: 0.8876 (p0) cc_final: 0.8621 (p0) REVERT: C 298 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8465 (mttm) REVERT: C 321 LYS cc_start: 0.7437 (mttt) cc_final: 0.6670 (tmtt) REVERT: C 336 GLN cc_start: 0.7839 (mt0) cc_final: 0.6978 (tt0) REVERT: C 343 LYS cc_start: 0.8462 (mttt) cc_final: 0.8246 (mtpt) REVERT: C 348 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8081 (t0) REVERT: C 349 ARG cc_start: 0.7091 (mtp180) cc_final: 0.5941 (mmm160) REVERT: C 379 ARG cc_start: 0.6740 (mtt180) cc_final: 0.6354 (mmm-85) outliers start: 15 outliers final: 9 residues processed: 51 average time/residue: 0.1835 time to fit residues: 10.8269 Evaluate side-chains 62 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 305 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 379 ARG 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 16 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.0670 chunk 13 optimal weight: 0.4980 chunk 11 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2472 Z= 0.149 Angle : 0.613 6.845 3303 Z= 0.299 Chirality : 0.050 0.126 372 Planarity : 0.002 0.023 423 Dihedral : 5.581 24.504 327 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: -3.43 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 299 PHE 0.004 0.001 PHE A 378 TYR 0.013 0.002 TYR B 310 ARG 0.000 0.000 ARG B 349 *********************** 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 58 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.314 Fit side-chains REVERT: A 295 ASP cc_start: 0.8316 (p0) cc_final: 0.7892 (p0) REVERT: A 321 LYS cc_start: 0.7270 (mttt) cc_final: 0.6783 (tmtt) REVERT: A 343 LYS cc_start: 0.8329 (mttt) cc_final: 0.7973 (mtpt) REVERT: A 372 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7111 (mp0) REVERT: A 376 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7758 (tt) REVERT: B 295 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7797 (p0) REVERT: B 325 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.6754 (pt) REVERT: B 338 GLU cc_start: 0.8137 (mp0) cc_final: 0.7824 (mp0) REVERT: B 358 ASP cc_start: 0.7912 (t0) cc_final: 0.7529 (t0) REVERT: B 372 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7254 (mp0) REVERT: C 276 GLN cc_start: 0.7048 (mt0) cc_final: 0.6214 (mp10) REVERT: C 321 LYS cc_start: 0.7205 (mttt) cc_final: 0.6402 (tmtt) REVERT: C 336 GLN cc_start: 0.7796 (mt0) cc_final: 0.6985 (tt0) REVERT: C 343 LYS cc_start: 0.8502 (mttt) cc_final: 0.8301 (mtpt) REVERT: C 348 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8261 (t0) REVERT: C 349 ARG cc_start: 0.7041 (mtp180) cc_final: 0.5854 (mmm160) REVERT: C 379 ARG cc_start: 0.6614 (mtt180) cc_final: 0.6268 (mmm-85) outliers start: 11 outliers final: 3 residues processed: 50 average time/residue: 0.1925 time to fit residues: 11.1648 Evaluate side-chains 49 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2472 Z= 0.310 Angle : 0.716 10.455 3303 Z= 0.347 Chirality : 0.052 0.142 372 Planarity : 0.003 0.026 423 Dihedral : 6.025 25.093 327 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 3.55 % Allowed : 10.64 % Favored : 85.82 % 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: -3.52 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.006 0.001 PHE B 378 TYR 0.024 0.004 TYR B 310 ARG 0.001 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 54 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.292 Fit side-chains REVERT: A 295 ASP cc_start: 0.8339 (p0) cc_final: 0.7871 (p0) REVERT: A 321 LYS cc_start: 0.7292 (mttt) cc_final: 0.6811 (tmtt) REVERT: A 343 LYS cc_start: 0.8275 (mttt) cc_final: 0.7906 (mtpt) REVERT: A 358 ASP cc_start: 0.7640 (t0) cc_final: 0.7393 (t0) REVERT: A 372 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7250 (mp0) REVERT: A 376 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7799 (tt) REVERT: B 295 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7769 (p0) REVERT: B 325 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.6818 (pt) REVERT: B 338 GLU cc_start: 0.8159 (mp0) cc_final: 0.7839 (mp0) REVERT: B 358 ASP cc_start: 0.8091 (t0) cc_final: 0.7657 (t0) REVERT: B 372 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7215 (mp0) REVERT: C 276 GLN cc_start: 0.7258 (mt0) cc_final: 0.6525 (mp10) REVERT: C 321 LYS cc_start: 0.7176 (mttt) cc_final: 0.6401 (tmtt) REVERT: C 338 GLU cc_start: 0.7429 (mp0) cc_final: 0.7153 (mp0) REVERT: C 343 LYS cc_start: 0.8470 (mttt) cc_final: 0.8250 (mtpt) REVERT: C 348 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8264 (t0) REVERT: C 349 ARG cc_start: 0.7014 (mtp180) cc_final: 0.5825 (mmm160) REVERT: C 379 ARG cc_start: 0.6718 (mtt180) cc_final: 0.6294 (mmm-85) outliers start: 10 outliers final: 4 residues processed: 48 average time/residue: 0.1835 time to fit residues: 10.2412 Evaluate side-chains 51 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 0.0060 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2472 Z= 0.206 Angle : 0.662 9.504 3303 Z= 0.319 Chirality : 0.050 0.145 372 Planarity : 0.003 0.025 423 Dihedral : 5.784 24.482 327 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.48 % Allowed : 11.35 % 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: -3.45 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (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 0.020 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 45 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.325 Fit side-chains REVERT: A 295 ASP cc_start: 0.8253 (p0) cc_final: 0.7882 (p0) REVERT: A 321 LYS cc_start: 0.7220 (mttt) cc_final: 0.6738 (tmtt) REVERT: A 343 LYS cc_start: 0.8270 (mttt) cc_final: 0.7903 (mtpt) REVERT: A 372 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7128 (mp0) REVERT: A 376 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7760 (tt) REVERT: B 338 GLU cc_start: 0.8124 (mp0) cc_final: 0.7796 (mp0) REVERT: B 358 ASP cc_start: 0.7966 (t0) cc_final: 0.7516 (t0) REVERT: B 372 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7178 (mp0) REVERT: C 276 GLN cc_start: 0.7067 (mt0) cc_final: 0.6332 (mp10) REVERT: C 338 GLU cc_start: 0.7456 (mp0) cc_final: 0.7153 (mp0) REVERT: C 343 LYS cc_start: 0.8503 (mttt) cc_final: 0.8261 (mtpt) REVERT: C 348 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8252 (t0) REVERT: C 349 ARG cc_start: 0.7055 (mtp180) cc_final: 0.5820 (mmm160) REVERT: C 379 ARG cc_start: 0.6704 (mtt180) cc_final: 0.6354 (mmm-85) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.1941 time to fit residues: 9.3521 Evaluate side-chains 43 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 376 LEU 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 7 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2472 Z= 0.164 Angle : 0.677 10.541 3303 Z= 0.319 Chirality : 0.051 0.169 372 Planarity : 0.003 0.023 423 Dihedral : 5.505 24.207 327 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.48 % Allowed : 11.70 % Favored : 85.82 % 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 A 330 PHE 0.003 0.001 PHE C 378 TYR 0.019 0.003 TYR B 310 ARG 0.000 0.000 ARG C 379 ********************** 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 50 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.328 Fit side-chains REVERT: A 295 ASP cc_start: 0.8199 (p0) cc_final: 0.7962 (p0) REVERT: A 321 LYS cc_start: 0.7245 (mttt) cc_final: 0.6696 (tmtt) REVERT: A 343 LYS cc_start: 0.8269 (mttt) cc_final: 0.7903 (mtpt) REVERT: A 372 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7090 (mp0) REVERT: A 376 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7691 (tt) REVERT: B 298 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8373 (mttt) REVERT: B 338 GLU cc_start: 0.8135 (mp0) cc_final: 0.7818 (mp0) REVERT: B 358 ASP cc_start: 0.8098 (t0) cc_final: 0.7665 (t0) REVERT: B 372 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7274 (mp0) REVERT: C 276 GLN cc_start: 0.7094 (mt0) cc_final: 0.6302 (mp10) REVERT: C 338 GLU cc_start: 0.7434 (mp0) cc_final: 0.7125 (mp0) REVERT: C 343 LYS cc_start: 0.8498 (mttt) cc_final: 0.8274 (mtpt) REVERT: C 348 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8260 (t0) REVERT: C 349 ARG cc_start: 0.7063 (mtp180) cc_final: 0.5833 (mmm160) REVERT: C 379 ARG cc_start: 0.6649 (mtt180) cc_final: 0.6299 (mmm-85) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.1846 time to fit residues: 10.1052 Evaluate side-chains 47 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 305 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0470 chunk 16 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- 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 = 0.4677 r_free = 0.4677 target = 0.232181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.195295 restraints weight = 2989.561| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.44 r_work: 0.4084 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2472 Z= 0.189 Angle : 0.660 10.582 3303 Z= 0.315 Chirality : 0.050 0.196 372 Planarity : 0.003 0.028 423 Dihedral : 5.556 24.542 327 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.84 % Allowed : 12.06 % 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: -3.33 (0.40), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (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 C 378 TYR 0.020 0.003 TYR B 310 ARG 0.000 0.000 ARG C 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.05 seconds wall clock time: 21 minutes 33.15 seconds (1293.15 seconds total)