Starting phenix.real_space_refine on Tue Mar 3 11:02:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tjo_10512/03_2026/6tjo_10512.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tjo_10512/03_2026/6tjo_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_2026/6tjo_10512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tjo_10512/03_2026/6tjo_10512.map" model { file = "/net/cci-nas-00/data/ceres_data/6tjo_10512/03_2026/6tjo_10512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tjo_10512/03_2026/6tjo_10512.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: B, C Time building chain proxies: 0.46, per 1000 atoms: 0.19 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: 0.18 Conformation dependent library (CDL) restraints added in 80.2 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: 0.07 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: 0.26 Time building geometry restraints manager: 0.25 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: 0.00 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: 1.100 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.490 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.690 ------------------------------------------------------------------------------- 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= 0.518 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.004 0.001 ARG A 379 TYR 0.011 0.005 TYR C 310 PHE 0.010 0.003 PHE B 378 HIS 0.011 0.005 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.01306 ( 2472) covalent geometry : angle 1.18250 ( 3303) hydrogen bonds : bond 0.11791 ( 10) hydrogen bonds : angle 7.00163 ( 30) *********************** 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 : 0.063 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: 0.7739 (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: 0.8442 (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: 0.0491 time to fit residues: 2.9318 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 : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4675 r_free = 0.4675 target = 0.229486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.195285 restraints weight = 2911.908| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.52 r_work: 0.4072 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1797 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= 0.145 Angle : 0.644 5.978 3303 Z= 0.330 Chirality : 0.052 0.132 372 Planarity : 0.005 0.039 423 Dihedral : 6.251 24.878 327 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.48 % Allowed : 7.09 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.018 0.004 TYR B 310 PHE 0.006 0.001 PHE A 378 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2472) covalent geometry : angle 0.64416 ( 3303) hydrogen bonds : bond 0.01952 ( 10) hydrogen bonds : angle 4.91067 ( 30) *********************** 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 57 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8776 (p0) cc_final: 0.8573 (p0) REVERT: A 321 LYS cc_start: 0.8027 (mttt) cc_final: 0.7454 (tmtt) REVERT: A 343 LYS cc_start: 0.8512 (mttt) cc_final: 0.8261 (mtpt) REVERT: B 295 ASP cc_start: 0.8662 (p0) cc_final: 0.8043 (p0) REVERT: B 348 ASP cc_start: 0.8529 (m-30) cc_final: 0.7119 (p0) REVERT: B 358 ASP cc_start: 0.7898 (t0) cc_final: 0.7610 (t0) REVERT: C 321 LYS cc_start: 0.8052 (mttt) cc_final: 0.7275 (tptp) REVERT: C 348 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8068 (t0) REVERT: C 349 ARG cc_start: 0.7549 (mtp180) cc_final: 0.6390 (mmm160) REVERT: C 379 ARG cc_start: 0.7048 (mtt180) cc_final: 0.6795 (mmm-85) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.0653 time to fit residues: 3.8666 Evaluate side-chains 49 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.078 ------------------------------------------------------------------------------- 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 6 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.121296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.101055 restraints weight = 3532.999| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.20 r_work: 0.3936 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2472 Z= 0.113 Angle : 0.635 6.629 3303 Z= 0.312 Chirality : 0.050 0.159 372 Planarity : 0.003 0.029 423 Dihedral : 5.706 23.880 327 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.55 % Allowed : 9.22 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.37), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.28), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 379 TYR 0.016 0.003 TYR B 310 PHE 0.004 0.001 PHE A 378 HIS 0.002 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2472) covalent geometry : angle 0.63543 ( 3303) hydrogen bonds : bond 0.01389 ( 10) hydrogen bonds : angle 4.48855 ( 30) *********************** 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 52 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7872 (mttt) cc_final: 0.7287 (tmtt) REVERT: A 343 LYS cc_start: 0.8423 (mttt) cc_final: 0.8097 (mtpp) REVERT: B 295 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.7888 (p0) REVERT: B 325 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7825 (mp) REVERT: B 338 GLU cc_start: 0.8419 (mp0) cc_final: 0.8206 (mp0) REVERT: B 348 ASP cc_start: 0.8436 (m-30) cc_final: 0.7114 (p0) REVERT: B 358 ASP cc_start: 0.7969 (t0) cc_final: 0.7709 (t0) REVERT: B 372 GLU cc_start: 0.7937 (mp0) cc_final: 0.7645 (mp0) REVERT: C 276 GLN cc_start: 0.7494 (mt0) cc_final: 0.6789 (mp10) REVERT: C 321 LYS cc_start: 0.7824 (mttt) cc_final: 0.7065 (tmtt) REVERT: C 349 ARG cc_start: 0.7571 (mtp180) cc_final: 0.6380 (mmm160) REVERT: C 379 ARG cc_start: 0.6889 (mtt180) cc_final: 0.6588 (mmm-85) outliers start: 10 outliers final: 4 residues processed: 45 average time/residue: 0.0881 time to fit residues: 4.4957 Evaluate side-chains 42 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.0570 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.099073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.077462 restraints weight = 3886.342| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.28 r_work: 0.3625 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2472 Z= 0.174 Angle : 0.662 7.723 3303 Z= 0.327 Chirality : 0.051 0.130 372 Planarity : 0.003 0.024 423 Dihedral : 5.921 24.101 327 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.55 % Allowed : 8.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.38), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.006 0.002 TYR B 310 PHE 0.005 0.001 PHE C 378 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 2472) covalent geometry : angle 0.66171 ( 3303) hydrogen bonds : bond 0.01419 ( 10) hydrogen bonds : angle 4.60931 ( 30) *********************** 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 48 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.095 Fit side-chains REVERT: A 321 LYS cc_start: 0.7431 (mttt) cc_final: 0.6849 (tmtt) REVERT: A 343 LYS cc_start: 0.8110 (mttt) cc_final: 0.7740 (mtpp) REVERT: B 295 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7959 (p0) REVERT: B 325 LEU cc_start: 0.7996 (mp) cc_final: 0.6836 (pt) REVERT: B 348 ASP cc_start: 0.8394 (m-30) cc_final: 0.6958 (p0) REVERT: B 358 ASP cc_start: 0.7998 (t0) cc_final: 0.7623 (t0) REVERT: B 372 GLU cc_start: 0.7837 (mp0) cc_final: 0.7398 (mp0) REVERT: C 276 GLN cc_start: 0.7325 (mt0) cc_final: 0.6662 (mp10) REVERT: C 321 LYS cc_start: 0.7383 (mttt) cc_final: 0.6607 (tmtt) REVERT: C 348 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7909 (t0) REVERT: C 349 ARG cc_start: 0.7277 (mtp180) cc_final: 0.6160 (mmm160) REVERT: C 379 ARG cc_start: 0.6630 (mtt180) cc_final: 0.6355 (mmm-85) outliers start: 10 outliers final: 6 residues processed: 41 average time/residue: 0.0881 time to fit residues: 4.1056 Evaluate side-chains 43 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 379 ARG 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 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 9 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.093111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.072238 restraints weight = 4092.417| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.15 r_work: 0.3511 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 2472 Z= 0.320 Angle : 0.792 6.768 3303 Z= 0.401 Chirality : 0.055 0.180 372 Planarity : 0.004 0.026 423 Dihedral : 6.684 25.779 327 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % Rotamer: Outliers : 3.90 % Allowed : 7.80 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.007 0.002 TYR A 310 PHE 0.008 0.002 PHE B 378 HIS 0.005 0.002 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00739 ( 2472) covalent geometry : angle 0.79167 ( 3303) hydrogen bonds : bond 0.01971 ( 10) hydrogen bonds : angle 4.60739 ( 30) *********************** 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 53 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.104 Fit side-chains REVERT: A 321 LYS cc_start: 0.7403 (mttt) cc_final: 0.6828 (tmtt) REVERT: A 343 LYS cc_start: 0.8219 (mttt) cc_final: 0.7859 (mtpt) REVERT: A 348 ASP cc_start: 0.8099 (t0) cc_final: 0.7877 (t0) REVERT: A 358 ASP cc_start: 0.7296 (t0) cc_final: 0.7093 (t0) REVERT: B 295 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7918 (p0) REVERT: B 325 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.6781 (pt) REVERT: B 338 GLU cc_start: 0.8423 (mp0) cc_final: 0.8192 (mp0) REVERT: B 358 ASP cc_start: 0.8123 (t0) cc_final: 0.7811 (t0) REVERT: C 276 GLN cc_start: 0.7380 (mt0) cc_final: 0.6692 (mp10) REVERT: C 321 LYS cc_start: 0.7572 (mttt) cc_final: 0.6777 (tptm) REVERT: C 338 GLU cc_start: 0.7489 (mp0) cc_final: 0.7207 (mp0) REVERT: C 348 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7951 (t0) REVERT: C 349 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6121 (mmm160) REVERT: C 379 ARG cc_start: 0.7020 (mtt180) cc_final: 0.6525 (mmm-85) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.0830 time to fit residues: 4.3087 Evaluate side-chains 52 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 379 ARG 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 325 LEU Chi-restraints excluded: chain C residue 343 LYS 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 1 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.098984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.077167 restraints weight = 3852.907| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.26 r_work: 0.3604 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2994 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= 0.145 Angle : 0.684 7.344 3303 Z= 0.332 Chirality : 0.051 0.139 372 Planarity : 0.002 0.020 423 Dihedral : 6.005 24.234 327 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.55 % Allowed : 8.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.006 0.002 TYR A 310 PHE 0.005 0.001 PHE C 378 HIS 0.002 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 2472) covalent geometry : angle 0.68423 ( 3303) hydrogen bonds : bond 0.01239 ( 10) hydrogen bonds : angle 4.11476 ( 30) *********************** 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 47 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.095 Fit side-chains REVERT: A 321 LYS cc_start: 0.7406 (mttt) cc_final: 0.6871 (tmtt) REVERT: A 343 LYS cc_start: 0.8173 (mttt) cc_final: 0.7817 (mtpt) REVERT: A 348 ASP cc_start: 0.8101 (t0) cc_final: 0.7889 (t0) REVERT: A 372 GLU cc_start: 0.7741 (mp0) cc_final: 0.7359 (mp0) REVERT: A 376 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7907 (tt) REVERT: B 295 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7837 (p0) REVERT: B 325 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.6650 (pt) REVERT: B 338 GLU cc_start: 0.8404 (mp0) cc_final: 0.8102 (mp0) REVERT: B 358 ASP cc_start: 0.8030 (t0) cc_final: 0.7620 (t0) REVERT: B 372 GLU cc_start: 0.7835 (mp0) cc_final: 0.7465 (mp0) REVERT: C 276 GLN cc_start: 0.7196 (mt0) cc_final: 0.6528 (mp10) REVERT: C 321 LYS cc_start: 0.7363 (mttt) cc_final: 0.6547 (tmtt) REVERT: C 348 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8038 (t0) REVERT: C 349 ARG cc_start: 0.7293 (mtp180) cc_final: 0.6064 (mmm160) REVERT: C 379 ARG cc_start: 0.6820 (mtt180) cc_final: 0.6391 (mmm-85) outliers start: 10 outliers final: 4 residues processed: 41 average time/residue: 0.0871 time to fit residues: 4.1007 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 : 0.096 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.109961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.090102 restraints weight = 3774.813| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.14 r_work: 0.3757 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3032 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= 0.220 Angle : 0.732 8.279 3303 Z= 0.357 Chirality : 0.052 0.179 372 Planarity : 0.003 0.021 423 Dihedral : 6.241 24.591 327 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 3.19 % Allowed : 8.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.005 0.001 TYR A 310 PHE 0.005 0.001 PHE A 378 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 2472) covalent geometry : angle 0.73233 ( 3303) hydrogen bonds : bond 0.01399 ( 10) hydrogen bonds : angle 4.17669 ( 30) *********************** 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 47 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.104 Fit side-chains REVERT: A 321 LYS cc_start: 0.7830 (mttt) cc_final: 0.7281 (tmtt) REVERT: A 343 LYS cc_start: 0.8558 (mttt) cc_final: 0.8238 (mtpt) REVERT: A 345 ASP cc_start: 0.8307 (m-30) cc_final: 0.7602 (t0) REVERT: A 358 ASP cc_start: 0.7501 (t0) cc_final: 0.7262 (t0) REVERT: B 295 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7810 (p0) REVERT: B 325 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6565 (pt) REVERT: B 338 GLU cc_start: 0.8429 (mp0) cc_final: 0.8203 (mp0) REVERT: B 358 ASP cc_start: 0.8124 (t0) cc_final: 0.7841 (t0) REVERT: C 276 GLN cc_start: 0.7612 (mt0) cc_final: 0.7058 (mp10) REVERT: C 321 LYS cc_start: 0.7821 (mttt) cc_final: 0.7036 (tmtt) REVERT: C 336 GLN cc_start: 0.8120 (mt0) cc_final: 0.7363 (tt0) REVERT: C 348 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8338 (t0) REVERT: C 349 ARG cc_start: 0.7560 (mtp180) cc_final: 0.6316 (mmm160) REVERT: C 379 ARG cc_start: 0.7149 (mtt180) cc_final: 0.6712 (mmm-85) outliers start: 9 outliers final: 5 residues processed: 42 average time/residue: 0.0883 time to fit residues: 4.2540 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 : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 379 ARG 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 10 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 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 = 0.4184 r_free = 0.4184 target = 0.108702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.088645 restraints weight = 3804.749| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.14 r_work: 0.3733 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2472 Z= 0.246 Angle : 0.761 9.325 3303 Z= 0.371 Chirality : 0.053 0.178 372 Planarity : 0.003 0.021 423 Dihedral : 6.395 24.912 327 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 3.55 % Allowed : 8.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.006 0.001 TYR C 310 PHE 0.007 0.001 PHE A 378 HIS 0.004 0.002 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 2472) covalent geometry : angle 0.76098 ( 3303) hydrogen bonds : bond 0.01460 ( 10) hydrogen bonds : angle 4.19780 ( 30) *********************** 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: 10 poor density : 39 time to evaluate : 0.110 Fit side-chains REVERT: A 321 LYS cc_start: 0.7834 (mttt) cc_final: 0.7278 (tmtt) REVERT: A 343 LYS cc_start: 0.8564 (mttt) cc_final: 0.8259 (mtpt) REVERT: A 345 ASP cc_start: 0.8301 (m-30) cc_final: 0.7598 (t0) REVERT: A 358 ASP cc_start: 0.7598 (t0) cc_final: 0.7380 (t0) REVERT: B 295 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7797 (p0) REVERT: B 325 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6542 (pt) REVERT: B 338 GLU cc_start: 0.8490 (mp0) cc_final: 0.8253 (mp0) REVERT: B 358 ASP cc_start: 0.8153 (t0) cc_final: 0.7884 (t0) REVERT: C 276 GLN cc_start: 0.7670 (mt0) cc_final: 0.7132 (mp10) REVERT: C 321 LYS cc_start: 0.7847 (mttt) cc_final: 0.7069 (tmtt) REVERT: C 348 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8538 (t0) REVERT: C 349 ARG cc_start: 0.7538 (mtp180) cc_final: 0.6274 (mmm160) REVERT: C 379 ARG cc_start: 0.7186 (mtt180) cc_final: 0.6712 (mmm-85) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.0845 time to fit residues: 4.1112 Evaluate side-chains 48 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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 379 ARG 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 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 8 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.113171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.092879 restraints weight = 3746.805| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.20 r_work: 0.3809 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2472 Z= 0.164 Angle : 0.730 10.286 3303 Z= 0.349 Chirality : 0.051 0.178 372 Planarity : 0.002 0.022 423 Dihedral : 6.008 24.040 327 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.84 % Allowed : 9.93 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (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 ARG 0.000 0.000 ARG C 379 TYR 0.009 0.002 TYR B 310 PHE 0.005 0.001 PHE B 378 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 2472) covalent geometry : angle 0.73004 ( 3303) hydrogen bonds : bond 0.01250 ( 10) hydrogen bonds : angle 3.91722 ( 30) *********************** 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 46 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.101 Fit side-chains REVERT: A 321 LYS cc_start: 0.7802 (mttt) cc_final: 0.7267 (tmtt) REVERT: A 343 LYS cc_start: 0.8559 (mttt) cc_final: 0.8255 (mtpt) REVERT: A 345 ASP cc_start: 0.8383 (m-30) cc_final: 0.7632 (t0) REVERT: A 372 GLU cc_start: 0.7969 (mp0) cc_final: 0.7725 (mp0) REVERT: B 295 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7647 (p0) REVERT: B 325 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6333 (pt) REVERT: B 338 GLU cc_start: 0.8463 (mp0) cc_final: 0.8227 (mp0) REVERT: B 358 ASP cc_start: 0.8096 (t0) cc_final: 0.7809 (t0) REVERT: C 276 GLN cc_start: 0.7619 (mt0) cc_final: 0.7094 (mp10) REVERT: C 321 LYS cc_start: 0.7741 (mttt) cc_final: 0.6988 (tmtt) REVERT: C 348 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8526 (t0) REVERT: C 349 ARG cc_start: 0.7513 (mtp180) cc_final: 0.6272 (mmm160) REVERT: C 379 ARG cc_start: 0.7173 (mtt180) cc_final: 0.6765 (mmm-85) outliers start: 8 outliers final: 4 residues processed: 41 average time/residue: 0.0866 time to fit residues: 4.1103 Evaluate side-chains 44 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.0000 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.117350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.096719 restraints weight = 3702.399| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.27 r_work: 0.3877 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2472 Z= 0.127 Angle : 0.712 11.119 3303 Z= 0.337 Chirality : 0.051 0.182 372 Planarity : 0.002 0.025 423 Dihedral : 5.700 23.629 327 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.48 % Allowed : 10.28 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.009 0.002 TYR A 310 PHE 0.004 0.001 PHE A 378 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2472) covalent geometry : angle 0.71161 ( 3303) hydrogen bonds : bond 0.01122 ( 10) hydrogen bonds : angle 3.73709 ( 30) ********************** 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 46 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7721 (mttt) cc_final: 0.7177 (tmtt) REVERT: A 343 LYS cc_start: 0.8550 (mttt) cc_final: 0.8265 (mtpt) REVERT: A 372 GLU cc_start: 0.7943 (mp0) cc_final: 0.7701 (mp0) REVERT: B 295 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7669 (p0) REVERT: B 338 GLU cc_start: 0.8327 (mp0) cc_final: 0.8118 (mp0) REVERT: B 358 ASP cc_start: 0.8088 (t0) cc_final: 0.7777 (t0) REVERT: C 276 GLN cc_start: 0.7630 (mt0) cc_final: 0.7096 (mp10) REVERT: C 348 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8511 (t0) REVERT: C 349 ARG cc_start: 0.7543 (mtp180) cc_final: 0.6245 (mmm160) REVERT: C 379 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6743 (mmm-85) outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.0812 time to fit residues: 3.9596 Evaluate side-chains 42 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.072 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.109184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.089535 restraints weight = 3830.832| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.04 r_work: 0.3724 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2472 Z= 0.186 Angle : 0.729 10.848 3303 Z= 0.352 Chirality : 0.051 0.175 372 Planarity : 0.003 0.023 423 Dihedral : 5.979 23.774 327 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.77 % Allowed : 11.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.000 0.000 ARG A 349 TYR 0.007 0.002 TYR A 310 PHE 0.005 0.001 PHE A 378 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 2472) covalent geometry : angle 0.72933 ( 3303) hydrogen bonds : bond 0.01384 ( 10) hydrogen bonds : angle 3.80522 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 830.12 seconds wall clock time: 15 minutes 13.32 seconds (913.32 seconds total)