Starting phenix.real_space_refine on Tue Mar 3 11:36:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x13_21987/03_2026/6x13_21987.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x13_21987/03_2026/6x13_21987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x13_21987/03_2026/6x13_21987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x13_21987/03_2026/6x13_21987.map" model { file = "/net/cci-nas-00/data/ceres_data/6x13_21987/03_2026/6x13_21987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x13_21987/03_2026/6x13_21987.cif" } resolution = 3.66 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 18 5.16 5 C 2067 2.51 5 N 501 2.21 5 O 549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3136 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3094 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 0.74, per 1000 atoms: 0.24 Number of scatterers: 3136 At special positions: 0 Unit cell: (66.5415, 78.3473, 71.9078, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 1 15.00 O 549 8.00 N 501 7.00 C 2067 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: 0.23 Conformation dependent library (CDL) restraints added in 106.8 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 85.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 11 through 33 Processing helix chain 'A' and resid 36 through 72 removed outlier: 3.767A pdb=" N TYR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.340A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET A 59 " --> pdb=" O CYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.929A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.811A pdb=" N LEU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 107 removed outlier: 4.218A pdb=" N LYS A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 174 through 220 removed outlier: 3.850A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.771A pdb=" N TYR A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 4.362A pdb=" N GLU A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.974A pdb=" N PHE A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 295 through 309 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 334 through 349 Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 376 through 418 removed outlier: 3.754A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 771 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: 0.50 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 482 1.31 - 1.43: 788 1.43 - 1.56: 1878 1.56 - 1.68: 14 1.68 - 1.81: 34 Bond restraints: 3196 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sigma weight residual 1.331 1.410 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C39 6OU A 501 " pdb=" C40 6OU A 501 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C15 6OU A 501 " pdb=" C16 6OU A 501 " ideal model delta sigma weight residual 1.501 1.562 -0.061 2.00e-02 2.50e+03 9.21e+00 bond pdb=" C38 6OU A 501 " pdb=" C39 6OU A 501 " ideal model delta sigma weight residual 1.530 1.580 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 3191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 4263 3.09 - 6.17: 67 6.17 - 9.26: 15 9.26 - 12.35: 3 12.35 - 15.43: 1 Bond angle restraints: 4349 Sorted by residual: angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 109.38 -15.43 3.00e+00 1.11e-01 2.65e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 120.46 -10.65 2.21e+00 2.05e-01 2.32e+01 angle pdb=" N GLY A 357 " pdb=" CA GLY A 357 " pdb=" C GLY A 357 " ideal model delta sigma weight residual 113.18 121.87 -8.69 2.37e+00 1.78e-01 1.34e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 120.48 -6.58 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C THR A 275 " pdb=" N ARG A 276 " pdb=" CA ARG A 276 " ideal model delta sigma weight residual 122.08 127.30 -5.22 1.47e+00 4.63e-01 1.26e+01 ... (remaining 4344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.76: 1768 25.76 - 51.51: 101 51.51 - 77.27: 16 77.27 - 103.03: 2 103.03 - 128.78: 2 Dihedral angle restraints: 1889 sinusoidal: 707 harmonic: 1182 Sorted by residual: dihedral pdb=" CA LEU A 372 " pdb=" C LEU A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C09 6OU A 501 " pdb=" C10 6OU A 501 " pdb=" C11 6OU A 501 " pdb=" C12 6OU A 501 " ideal model delta sinusoidal sigma weight residual 179.71 -51.51 -128.78 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C20 6OU A 501 " pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " pdb=" C33 6OU A 501 " ideal model delta sinusoidal sigma weight residual -177.41 -63.97 -113.44 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 1886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 347 0.040 - 0.080: 138 0.080 - 0.119: 43 0.119 - 0.159: 7 0.159 - 0.199: 5 Chirality restraints: 540 Sorted by residual: chirality pdb=" C20 6OU A 501 " pdb=" C19 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O30 6OU A 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA LEU A 303 " pdb=" N LEU A 303 " pdb=" C LEU A 303 " pdb=" CB LEU A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA ALA A 205 " pdb=" N ALA A 205 " pdb=" C ALA A 205 " pdb=" CB ALA A 205 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 537 not shown) Planarity restraints: 533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO A 45 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 243 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C ILE A 243 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 243 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 244 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 303 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO A 304 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.031 5.00e-02 4.00e+02 ... (remaining 530 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1023 2.85 - 3.36: 3072 3.36 - 3.88: 5111 3.88 - 4.39: 5458 4.39 - 4.90: 9825 Nonbonded interactions: 24489 Sorted by model distance: nonbonded pdb=" O LYS A 414 " pdb=" OG1 THR A 418 " model vdw 2.340 3.040 nonbonded pdb=" OD1 ASP A 390 " pdb=" NH1 ARG A 397 " model vdw 2.402 3.120 nonbonded pdb=" O GLU A 296 " pdb=" OG SER A 300 " model vdw 2.438 3.040 nonbonded pdb=" NZ LYS A 196 " pdb=" O24 6OU A 501 " model vdw 2.439 3.120 nonbonded pdb=" O SER A 171 " pdb=" NH2 ARG A 177 " model vdw 2.454 3.120 ... (remaining 24484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.870 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.007 0.086 3196 Z= 0.324 Angle : 1.044 15.434 4349 Z= 0.516 Chirality : 0.048 0.199 540 Planarity : 0.008 0.065 533 Dihedral : 16.899 128.781 1141 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.31 % Allowed : 9.23 % Favored : 90.46 % Cbeta Deviations : 0.27 % 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: -3.73 (0.31), residues: 415 helix: -2.04 (0.20), residues: 351 sheet: None (None), residues: 0 loop : -3.62 (0.61), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.017 0.002 TYR A 299 PHE 0.009 0.001 PHE A 210 HIS 0.002 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00674 ( 3196) covalent geometry : angle 1.04377 ( 4349) hydrogen bonds : bond 0.12122 ( 258) hydrogen bonds : angle 6.03712 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.108 Fit side-chains REVERT: A 35 TYR cc_start: 0.7029 (m-80) cc_final: 0.6827 (m-10) REVERT: A 59 MET cc_start: 0.9460 (tpp) cc_final: 0.9200 (mmm) REVERT: A 202 MET cc_start: 0.8192 (mmm) cc_final: 0.7863 (mmm) REVERT: A 362 MET cc_start: 0.7455 (ttm) cc_final: 0.7149 (ttm) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.0726 time to fit residues: 5.3747 Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110936 restraints weight = 4122.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113204 restraints weight = 2751.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115084 restraints weight = 2103.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116079 restraints weight = 1744.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.116956 restraints weight = 1550.825| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3196 Z= 0.169 Angle : 0.643 6.927 4349 Z= 0.333 Chirality : 0.040 0.150 540 Planarity : 0.006 0.069 533 Dihedral : 11.662 96.057 481 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.92 % Allowed : 13.85 % Favored : 85.23 % 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: -0.86 (0.39), residues: 415 helix: 0.11 (0.26), residues: 350 sheet: None (None), residues: 0 loop : -3.93 (0.56), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 397 TYR 0.036 0.002 TYR A 299 PHE 0.007 0.001 PHE A 273 HIS 0.001 0.000 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3196) covalent geometry : angle 0.64267 ( 4349) hydrogen bonds : bond 0.05592 ( 258) hydrogen bonds : angle 4.56161 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.110 Fit side-chains REVERT: A 35 TYR cc_start: 0.7042 (m-80) cc_final: 0.6754 (m-10) REVERT: A 169 MET cc_start: 0.8605 (tpp) cc_final: 0.7858 (ttm) REVERT: A 202 MET cc_start: 0.8286 (mmm) cc_final: 0.7887 (mmm) REVERT: A 362 MET cc_start: 0.7350 (ttm) cc_final: 0.6890 (ttm) outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.0616 time to fit residues: 4.3658 Evaluate side-chains 52 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.126498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.100997 restraints weight = 4222.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.103165 restraints weight = 2974.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.104729 restraints weight = 2356.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.105579 restraints weight = 2014.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.106222 restraints weight = 1829.024| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3196 Z= 0.166 Angle : 0.626 6.464 4349 Z= 0.324 Chirality : 0.039 0.143 540 Planarity : 0.005 0.074 533 Dihedral : 9.623 93.347 481 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.54 % Allowed : 15.69 % Favored : 82.77 % 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: 0.28 (0.41), residues: 415 helix: 0.84 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.39 (0.63), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 397 TYR 0.031 0.002 TYR A 299 PHE 0.009 0.001 PHE A 273 HIS 0.001 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3196) covalent geometry : angle 0.62625 ( 4349) hydrogen bonds : bond 0.05395 ( 258) hydrogen bonds : angle 4.40337 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.117 Fit side-chains REVERT: A 35 TYR cc_start: 0.6959 (m-80) cc_final: 0.6681 (m-10) REVERT: A 169 MET cc_start: 0.8553 (tpp) cc_final: 0.7914 (ttm) REVERT: A 362 MET cc_start: 0.7445 (ttm) cc_final: 0.6941 (ttm) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.0565 time to fit residues: 4.5086 Evaluate side-chains 53 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 36 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.127508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101421 restraints weight = 4209.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103603 restraints weight = 2933.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.105220 restraints weight = 2313.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.106226 restraints weight = 1968.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106822 restraints weight = 1771.675| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3196 Z= 0.153 Angle : 0.617 7.983 4349 Z= 0.315 Chirality : 0.039 0.140 540 Planarity : 0.005 0.074 533 Dihedral : 8.168 80.340 481 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.15 % Allowed : 17.54 % Favored : 80.31 % 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: 0.85 (0.42), residues: 415 helix: 1.23 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.24 (0.65), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.038 0.002 TYR A 299 PHE 0.008 0.001 PHE A 273 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3196) covalent geometry : angle 0.61716 ( 4349) hydrogen bonds : bond 0.05149 ( 258) hydrogen bonds : angle 4.34589 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.109 Fit side-chains REVERT: A 169 MET cc_start: 0.8536 (tpp) cc_final: 0.7884 (ttm) REVERT: A 202 MET cc_start: 0.8116 (mmm) cc_final: 0.7564 (mmm) REVERT: A 276 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8013 (mtm-85) REVERT: A 298 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8191 (tt) REVERT: A 362 MET cc_start: 0.7495 (ttm) cc_final: 0.6973 (ttm) outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 0.0569 time to fit residues: 4.4456 Evaluate side-chains 53 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.097030 restraints weight = 4227.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.099029 restraints weight = 3044.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100428 restraints weight = 2444.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.101251 restraints weight = 2107.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101781 restraints weight = 1918.150| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3196 Z= 0.197 Angle : 0.660 6.608 4349 Z= 0.341 Chirality : 0.040 0.141 540 Planarity : 0.005 0.077 533 Dihedral : 8.142 84.233 481 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.77 % Allowed : 20.00 % Favored : 77.23 % 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: 0.95 (0.42), residues: 415 helix: 1.31 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.20 (0.65), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.036 0.002 TYR A 299 PHE 0.010 0.001 PHE A 273 HIS 0.002 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 3196) covalent geometry : angle 0.65970 ( 4349) hydrogen bonds : bond 0.05683 ( 258) hydrogen bonds : angle 4.45595 ( 771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.114 Fit side-chains REVERT: A 103 MET cc_start: 0.8676 (tpp) cc_final: 0.8347 (mmm) REVERT: A 169 MET cc_start: 0.8569 (tpp) cc_final: 0.7941 (ttm) REVERT: A 215 TYR cc_start: 0.8115 (t80) cc_final: 0.7797 (t80) REVERT: A 298 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8272 (tt) REVERT: A 323 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7452 (t80) REVERT: A 362 MET cc_start: 0.7579 (ttm) cc_final: 0.7049 (ttm) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.0590 time to fit residues: 4.4099 Evaluate side-chains 55 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.122881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.097326 restraints weight = 4213.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099309 restraints weight = 2999.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100721 restraints weight = 2413.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.101594 restraints weight = 2085.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101845 restraints weight = 1885.933| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3196 Z= 0.177 Angle : 0.638 6.387 4349 Z= 0.330 Chirality : 0.040 0.140 540 Planarity : 0.005 0.081 533 Dihedral : 7.905 81.776 481 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.00 % Allowed : 19.69 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.42), residues: 415 helix: 1.48 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -2.95 (0.67), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.033 0.002 TYR A 299 PHE 0.010 0.001 PHE A 273 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3196) covalent geometry : angle 0.63787 ( 4349) hydrogen bonds : bond 0.05491 ( 258) hydrogen bonds : angle 4.38725 ( 771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.101 Fit side-chains REVERT: A 103 MET cc_start: 0.8660 (tpp) cc_final: 0.8347 (mmm) REVERT: A 169 MET cc_start: 0.8568 (tpp) cc_final: 0.7971 (ttm) REVERT: A 276 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.7968 (mtm-85) REVERT: A 298 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8286 (tt) REVERT: A 323 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7470 (t80) outliers start: 13 outliers final: 7 residues processed: 63 average time/residue: 0.0615 time to fit residues: 4.8185 Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 392 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.121883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.096109 restraints weight = 4248.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098120 restraints weight = 3016.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099612 restraints weight = 2406.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.100483 restraints weight = 2065.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100984 restraints weight = 1874.368| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3196 Z= 0.190 Angle : 0.657 6.786 4349 Z= 0.340 Chirality : 0.041 0.216 540 Planarity : 0.005 0.084 533 Dihedral : 7.978 82.562 481 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.69 % Allowed : 20.31 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.42), residues: 415 helix: 1.54 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -3.01 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.032 0.002 TYR A 299 PHE 0.010 0.001 PHE A 273 HIS 0.002 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 3196) covalent geometry : angle 0.65680 ( 4349) hydrogen bonds : bond 0.05657 ( 258) hydrogen bonds : angle 4.42514 ( 771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.109 Fit side-chains REVERT: A 169 MET cc_start: 0.8592 (tpp) cc_final: 0.8010 (ttm) REVERT: A 215 TYR cc_start: 0.8087 (t80) cc_final: 0.7860 (t80) REVERT: A 276 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.7909 (mtm-85) REVERT: A 298 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8279 (tt) REVERT: A 323 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7448 (t80) outliers start: 12 outliers final: 7 residues processed: 60 average time/residue: 0.0576 time to fit residues: 4.3733 Evaluate side-chains 57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 392 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.124736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099146 restraints weight = 4340.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.101176 restraints weight = 3041.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.102773 restraints weight = 2402.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.103685 restraints weight = 2052.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.103690 restraints weight = 1847.042| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3196 Z= 0.157 Angle : 0.638 8.993 4349 Z= 0.327 Chirality : 0.040 0.219 540 Planarity : 0.005 0.083 533 Dihedral : 7.612 75.915 481 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.08 % Allowed : 21.85 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.42), residues: 415 helix: 1.69 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -2.78 (0.70), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.033 0.002 TYR A 299 PHE 0.009 0.001 PHE A 273 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3196) covalent geometry : angle 0.63820 ( 4349) hydrogen bonds : bond 0.05200 ( 258) hydrogen bonds : angle 4.28819 ( 771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.116 Fit side-chains REVERT: A 169 MET cc_start: 0.8547 (tpp) cc_final: 0.7973 (ttm) REVERT: A 276 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.7988 (mtm-85) REVERT: A 298 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8266 (tt) REVERT: A 362 MET cc_start: 0.7540 (ttm) cc_final: 0.6949 (ttm) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.0542 time to fit residues: 4.4205 Evaluate side-chains 58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 392 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.141672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116084 restraints weight = 4259.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118698 restraints weight = 2707.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120747 restraints weight = 2049.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121839 restraints weight = 1705.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122675 restraints weight = 1517.774| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3196 Z= 0.159 Angle : 0.647 8.617 4349 Z= 0.331 Chirality : 0.041 0.229 540 Planarity : 0.005 0.083 533 Dihedral : 7.519 73.739 481 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.77 % Allowed : 22.77 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.43), residues: 415 helix: 1.70 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.55 (0.73), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.032 0.002 TYR A 299 PHE 0.009 0.001 PHE A 273 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3196) covalent geometry : angle 0.64703 ( 4349) hydrogen bonds : bond 0.05260 ( 258) hydrogen bonds : angle 4.28707 ( 771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.114 Fit side-chains REVERT: A 169 MET cc_start: 0.8525 (tpp) cc_final: 0.7986 (ttm) REVERT: A 276 ARG cc_start: 0.8414 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: A 298 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8245 (tt) REVERT: A 323 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7426 (t80) REVERT: A 362 MET cc_start: 0.7514 (ttm) cc_final: 0.6919 (ttm) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.0509 time to fit residues: 3.8781 Evaluate side-chains 60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 392 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101632 restraints weight = 4173.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103669 restraints weight = 2928.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.105228 restraints weight = 2324.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105928 restraints weight = 1995.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.106810 restraints weight = 1826.328| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3196 Z= 0.147 Angle : 0.640 8.703 4349 Z= 0.327 Chirality : 0.040 0.211 540 Planarity : 0.005 0.080 533 Dihedral : 7.262 67.889 481 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.46 % Allowed : 23.08 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.43), residues: 415 helix: 1.81 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.42 (0.73), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.032 0.002 TYR A 299 PHE 0.009 0.001 PHE A 273 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3196) covalent geometry : angle 0.64021 ( 4349) hydrogen bonds : bond 0.04959 ( 258) hydrogen bonds : angle 4.17780 ( 771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.095 Fit side-chains REVERT: A 169 MET cc_start: 0.8476 (tpp) cc_final: 0.7946 (ttm) REVERT: A 276 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7944 (mtm-85) REVERT: A 298 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 323 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7434 (t80) REVERT: A 362 MET cc_start: 0.7508 (ttm) cc_final: 0.6888 (ttm) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.0547 time to fit residues: 4.2310 Evaluate side-chains 58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.126587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.101947 restraints weight = 4272.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.103847 restraints weight = 3125.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.105081 restraints weight = 2518.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.106048 restraints weight = 2189.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.106766 restraints weight = 1972.854| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3196 Z= 0.148 Angle : 0.639 9.241 4349 Z= 0.327 Chirality : 0.040 0.173 540 Planarity : 0.005 0.077 533 Dihedral : 7.220 65.848 481 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.15 % Allowed : 23.08 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.43), residues: 415 helix: 1.85 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.33 (0.75), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.042 0.002 TYR A 299 PHE 0.008 0.001 PHE A 273 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3196) covalent geometry : angle 0.63866 ( 4349) hydrogen bonds : bond 0.05003 ( 258) hydrogen bonds : angle 4.21434 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 684.61 seconds wall clock time: 12 minutes 22.67 seconds (742.67 seconds total)