Starting phenix.real_space_refine on Thu Sep 10 20:54:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x13_21987/09_2026/6x13_21987.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x13_21987/09_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_21987/09_2026/6x13_21987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x13_21987/09_2026/6x13_21987.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x13_21987/09_2026/6x13_21987.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x13_21987/09_2026/6x13_21987.cif" model { file = "/net/cci-nas-00/data/ceres_data/6x13_21987/09_2026/6x13_21987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x13_21987/09_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-2.2.1-6174/lib/python3.11/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: 0.92, per 1000 atoms: 0.29 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: 0.30 Conformation dependent library (CDL) restraints added in 82.8 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: 0.08 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: 0.32 Time building geometry restraints manager: 0.32 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: 1765 25.76 - 51.51: 97 51.51 - 77.27: 13 77.27 - 103.03: 1 103.03 - 128.78: 2 Dihedral angle restraints: 1878 sinusoidal: 696 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 1875 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: 1.570 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.740 Find NCS groups from input model: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 16.269 128.781 1130 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/Z covalent geometry : bond 0.00674 / 0.32 ( 3196) covalent geometry : angle 1.04377 / 0.52 ( 4349) hydrogen bonds : bond 0.12122 / 7.65 ( 258) hydrogen bonds : angle 6.03712 / 4.10 ( 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 : 0.069 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: 0.0675 time to fit residues: 5.0698 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 : 0.091 ------------------------------------------------------------------------------- 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... 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 = 0.3495 r_free = 0.3495 target = 0.135152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110567 restraints weight = 4123.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112986 restraints weight = 2747.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114555 restraints weight = 2089.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115815 restraints weight = 1752.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.116554 restraints weight = 1556.130| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3196 Z= 0.170 Angle : 0.643 6.840 4349 Z= 0.334 Chirality : 0.040 0.153 540 Planarity : 0.006 0.070 533 Dihedral : 10.753 99.663 470 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.82 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: -0.85 (0.39), residues: 415 helix: 0.12 (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 0.035 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/Z covalent geometry : bond 0.00382 / 0.17 ( 3196) covalent geometry : angle 0.64265 / 0.33 ( 4349) hydrogen bonds : bond 0.05576 / 3.85 ( 258) hydrogen bonds : angle 4.57395 / 3.22 ( 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 : 0.127 Fit side-chains REVERT: A 35 TYR cc_start: 0.7040 (m-80) cc_final: 0.6754 (m-10) REVERT: A 202 MET cc_start: 0.8286 (mmm) cc_final: 0.7889 (mmm) REVERT: A 362 MET cc_start: 0.7340 (ttm) cc_final: 0.6885 (ttm) outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.0607 time to fit residues: 4.3337 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 : 0.110 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.0470 chunk 5 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114128 restraints weight = 4102.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.116543 restraints weight = 2743.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118098 restraints weight = 2097.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119404 restraints weight = 1769.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120261 restraints weight = 1559.404| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3196 Z= 0.136 Angle : 0.593 6.479 4349 Z= 0.307 Chirality : 0.038 0.139 540 Planarity : 0.005 0.073 533 Dihedral : 9.015 91.045 470 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.23 % Allowed : 14.77 % Favored : 84.00 % 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: 0.41 (0.42), residues: 415 helix: 0.96 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.50 (0.60), 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 0.007 0.001 PHE A 273 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 3196) covalent geometry : angle 0.59317 / 0.31 ( 4349) hydrogen bonds : bond 0.04918 / 3.43 ( 258) hydrogen bonds : angle 4.26455 / 3.03 ( 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 64 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.107 Fit side-chains REVERT: A 35 TYR cc_start: 0.6932 (m-80) cc_final: 0.6707 (m-10) REVERT: A 169 MET cc_start: 0.8338 (tpp) cc_final: 0.7826 (ttm) REVERT: A 202 MET cc_start: 0.8140 (mmm) cc_final: 0.7558 (mmm) REVERT: A 262 ILE cc_start: 0.8817 (tp) cc_final: 0.8494 (tp) REVERT: A 276 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8116 (mtm-85) REVERT: A 362 MET cc_start: 0.7338 (ttm) cc_final: 0.6913 (ttm) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.0497 time to fit residues: 4.1382 Evaluate side-chains 56 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.098569 restraints weight = 4257.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100659 restraints weight = 3009.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101785 restraints weight = 2398.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.102882 restraints weight = 2103.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.102882 restraints weight = 1916.288| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3196 Z= 0.170 Angle : 0.634 8.109 4349 Z= 0.324 Chirality : 0.040 0.142 540 Planarity : 0.005 0.074 533 Dihedral : 8.237 84.963 470 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.85 % Allowed : 18.77 % Favored : 79.38 % 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: 0.77 (0.42), residues: 415 helix: 1.18 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.25 (0.64), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 397 TYR 0.039 0.002 TYR A 299 PHE 0.010 0.001 PHE A 273 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 3196) covalent geometry : angle 0.63386 / 0.32 ( 4349) hydrogen bonds : bond 0.05346 / 3.75 ( 258) hydrogen bonds : angle 4.38407 / 3.13 ( 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 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.112 Fit side-chains REVERT: A 35 TYR cc_start: 0.6945 (m-80) cc_final: 0.6735 (m-10) REVERT: A 169 MET cc_start: 0.8423 (tpp) cc_final: 0.7854 (ttm) REVERT: A 215 TYR cc_start: 0.8105 (t80) cc_final: 0.7825 (t80) REVERT: A 298 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 362 MET cc_start: 0.7519 (ttm) cc_final: 0.6990 (ttm) outliers start: 6 outliers final: 2 residues processed: 59 average time/residue: 0.0521 time to fit residues: 3.8457 Evaluate side-chains 52 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.102012 restraints weight = 4181.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.104292 restraints weight = 2885.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105755 restraints weight = 2261.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106895 restraints weight = 1926.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107795 restraints weight = 1715.607| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3196 Z= 0.145 Angle : 0.606 6.942 4349 Z= 0.313 Chirality : 0.039 0.146 540 Planarity : 0.005 0.076 533 Dihedral : 7.663 79.097 470 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.15 % Allowed : 20.00 % Favored : 77.85 % 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: 1.17 (0.43), residues: 415 helix: 1.46 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.15 (0.66), 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 0.008 0.001 PHE A 261 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 3196) covalent geometry : angle 0.60560 / 0.31 ( 4349) hydrogen bonds : bond 0.04980 / 3.49 ( 258) hydrogen bonds : angle 4.24706 / 3.04 ( 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 60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.106 Fit side-chains REVERT: A 169 MET cc_start: 0.8369 (tpp) cc_final: 0.7827 (ttm) REVERT: A 298 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8185 (tt) REVERT: A 362 MET cc_start: 0.7494 (ttm) cc_final: 0.6948 (ttm) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.0566 time to fit residues: 4.2822 Evaluate side-chains 55 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 298 ILE 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: 0.9980 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113175 restraints weight = 4204.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.115937 restraints weight = 2718.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.117768 restraints weight = 2055.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118767 restraints weight = 1731.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119523 restraints weight = 1555.473| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1946 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= 0.188 Angle : 0.650 6.440 4349 Z= 0.337 Chirality : 0.041 0.141 540 Planarity : 0.005 0.079 533 Dihedral : 7.747 80.281 470 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.08 % Allowed : 19.08 % Favored : 77.85 % 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: 1.17 (0.42), residues: 415 helix: 1.48 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -3.06 (0.65), residues: 66 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 0.002 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 3196) covalent geometry : angle 0.64973 / 0.34 ( 4349) hydrogen bonds : bond 0.05547 / 3.91 ( 258) hydrogen bonds : angle 4.39537 / 3.14 ( 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 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.122 Fit side-chains REVERT: A 169 MET cc_start: 0.8414 (tpp) cc_final: 0.7872 (ttm) REVERT: A 215 TYR cc_start: 0.8097 (t80) cc_final: 0.7804 (t80) REVERT: A 298 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 323 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7479 (t80) outliers start: 10 outliers final: 3 residues processed: 58 average time/residue: 0.0627 time to fit residues: 4.5680 Evaluate side-chains 53 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.103114 restraints weight = 4334.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.105539 restraints weight = 2935.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107207 restraints weight = 2302.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108152 restraints weight = 1968.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.108912 restraints weight = 1781.349| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2027 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= 0.160 Angle : 0.630 8.799 4349 Z= 0.323 Chirality : 0.040 0.174 540 Planarity : 0.005 0.083 533 Dihedral : 7.579 76.183 470 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.15 % Allowed : 21.23 % Favored : 76.62 % 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: 1.41 (0.42), residues: 415 helix: 1.61 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -2.95 (0.68), 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/Z covalent geometry : bond 0.00362 / 0.16 ( 3196) covalent geometry : angle 0.63011 / 0.32 ( 4349) hydrogen bonds : bond 0.05231 / 3.68 ( 258) hydrogen bonds : angle 4.30832 / 3.08 ( 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 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.078 Fit side-chains REVERT: A 169 MET cc_start: 0.8385 (tpp) cc_final: 0.7870 (ttm) REVERT: A 215 TYR cc_start: 0.8078 (t80) cc_final: 0.7798 (t80) REVERT: A 298 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8183 (tt) REVERT: A 362 MET cc_start: 0.7531 (ttm) cc_final: 0.6962 (ttm) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 0.0577 time to fit residues: 4.3967 Evaluate side-chains 54 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 298 ILE 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: 0.8980 chunk 12 optimal weight: 0.0170 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.150706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126131 restraints weight = 4333.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128747 restraints weight = 2713.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130781 restraints weight = 2021.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132225 restraints weight = 1644.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132775 restraints weight = 1444.559| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3196 Z= 0.140 Angle : 0.663 14.729 4349 Z= 0.325 Chirality : 0.040 0.196 540 Planarity : 0.005 0.081 533 Dihedral : 7.059 68.265 470 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.46 % Allowed : 21.54 % 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: 1.70 (0.43), residues: 415 helix: 1.77 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.70 (0.72), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.034 0.002 TYR A 299 PHE 0.008 0.001 PHE A 273 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 3196) covalent geometry : angle 0.66262 / 0.33 ( 4349) hydrogen bonds : bond 0.04871 / 3.40 ( 258) hydrogen bonds : angle 4.17051 / 3.00 ( 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 63 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.116 Fit side-chains REVERT: A 169 MET cc_start: 0.8311 (tpp) cc_final: 0.7856 (ttm) REVERT: A 276 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.7988 (mtm-85) REVERT: A 298 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8207 (tt) REVERT: A 323 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7474 (t80) REVERT: A 362 MET cc_start: 0.7482 (ttm) cc_final: 0.6867 (ttm) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.0565 time to fit residues: 4.4055 Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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 323 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 25 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.0170 chunk 14 optimal weight: 0.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.105370 restraints weight = 4264.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.107183 restraints weight = 3078.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108630 restraints weight = 2500.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109728 restraints weight = 2163.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.110267 restraints weight = 1956.756| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3196 Z= 0.133 Angle : 0.641 10.604 4349 Z= 0.318 Chirality : 0.039 0.180 540 Planarity : 0.005 0.076 533 Dihedral : 6.254 57.009 470 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.15 % Allowed : 21.85 % 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: 1.97 (0.43), residues: 415 helix: 1.96 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.62 (0.73), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.043 0.002 TYR A 299 PHE 0.008 0.001 PHE A 273 HIS 0.001 0.000 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 3196) covalent geometry : angle 0.64143 / 0.32 ( 4349) hydrogen bonds : bond 0.04525 / 3.16 ( 258) hydrogen bonds : angle 4.10228 / 2.94 ( 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 67 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.065 Fit side-chains REVERT: A 169 MET cc_start: 0.8237 (tpp) cc_final: 0.7803 (ttm) REVERT: A 215 TYR cc_start: 0.7878 (t80) cc_final: 0.7655 (t80) REVERT: A 362 MET cc_start: 0.7470 (ttm) cc_final: 0.6866 (ttm) outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 0.0540 time to fit residues: 4.5825 Evaluate side-chains 60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 chunk 13 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.102888 restraints weight = 4246.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.104654 restraints weight = 3119.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.106085 restraints weight = 2543.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.107137 restraints weight = 2196.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107354 restraints weight = 1981.187| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3196 Z= 0.147 Angle : 0.663 11.483 4349 Z= 0.330 Chirality : 0.040 0.195 540 Planarity : 0.006 0.079 533 Dihedral : 6.234 52.628 470 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.23 % Allowed : 23.08 % Favored : 75.69 % 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: 1.92 (0.42), residues: 415 helix: 1.90 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.50 (0.73), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 276 TYR 0.037 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/Z covalent geometry : bond 0.00331 / 0.15 ( 3196) covalent geometry : angle 0.66307 / 0.33 ( 4349) hydrogen bonds : bond 0.04773 / 3.35 ( 258) hydrogen bonds : angle 4.17546 / 3.00 ( 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 57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.108 Fit side-chains REVERT: A 169 MET cc_start: 0.8282 (tpp) cc_final: 0.7821 (ttm) REVERT: A 215 TYR cc_start: 0.7990 (t80) cc_final: 0.7731 (t80) REVERT: A 323 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7497 (t80) REVERT: A 362 MET cc_start: 0.7504 (ttm) cc_final: 0.6890 (ttm) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.0630 time to fit residues: 4.3968 Evaluate side-chains 55 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 225 VAL 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: 0.1980 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104085 restraints weight = 4317.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.105986 restraints weight = 3130.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107453 restraints weight = 2522.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108261 restraints weight = 2196.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108563 restraints weight = 1996.948| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3196 Z= 0.145 Angle : 0.656 11.019 4349 Z= 0.326 Chirality : 0.040 0.175 540 Planarity : 0.006 0.077 533 Dihedral : 6.165 47.782 470 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.85 % Allowed : 22.46 % Favored : 75.69 % 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: 1.96 (0.42), residues: 415 helix: 1.93 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.43 (0.74), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 276 TYR 0.038 0.002 TYR A 299 PHE 0.010 0.001 PHE A 273 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 3196) covalent geometry : angle 0.65578 / 0.33 ( 4349) hydrogen bonds : bond 0.04807 / 3.37 ( 258) hydrogen bonds : angle 4.15102 / 2.97 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 712.26 seconds wall clock time: 12 minutes 57.15 seconds (777.15 seconds total)