Starting phenix.real_space_refine on Tue Feb 3 13:23:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ugu_64144/02_2026/9ugu_64144.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ugu_64144/02_2026/9ugu_64144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ugu_64144/02_2026/9ugu_64144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ugu_64144/02_2026/9ugu_64144.map" model { file = "/net/cci-nas-00/data/ceres_data/9ugu_64144/02_2026/9ugu_64144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ugu_64144/02_2026/9ugu_64144.cif" } resolution = 3.07 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= -0.001 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2088 2.51 5 N 507 2.21 5 O 559 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3175 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3175 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 16, 'TRANS': 399} Chain breaks: 1 Time building chain proxies: 0.86, per 1000 atoms: 0.27 Number of scatterers: 3175 At special positions: 0 Unit cell: (72.512, 58.504, 69.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 559 8.00 N 507 7.00 C 2088 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: 0.25 Conformation dependent library (CDL) restraints added in 124.7 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 74.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 1 through 22 removed outlier: 4.144A pdb=" N GLY A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 42 removed outlier: 3.582A pdb=" N VAL A 34 " --> pdb=" O THR A 30 " (cutoff:3.500A) Proline residue: A 36 - end of helix removed outlier: 3.974A pdb=" N GLU A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 60 removed outlier: 3.542A pdb=" N ILE A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.606A pdb=" N LEU A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 71' Processing helix chain 'A' and resid 77 through 93 removed outlier: 3.519A pdb=" N SER A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 97 removed outlier: 3.697A pdb=" N SER A 97 " --> pdb=" O PHE A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.599A pdb=" N ALA A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.514A pdb=" N LEU A 125 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.585A pdb=" N ILE A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 141' Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 173 through 187 removed outlier: 3.595A pdb=" N LEU A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 247 removed outlier: 3.927A pdb=" N TRP A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.704A pdb=" N GLU A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 removed outlier: 5.937A pdb=" N LYS A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 322 removed outlier: 3.561A pdb=" N LEU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 312 " --> pdb=" O MET A 308 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 357 Proline residue: A 345 - end of helix removed outlier: 3.511A pdb=" N GLY A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.868A pdb=" N CYS A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 379 removed outlier: 3.819A pdb=" N MET A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY A 376 " --> pdb=" O MET A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.781A pdb=" N ILE A 387 " --> pdb=" O PRO A 383 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 414 169 hydrogen bonds defined for protein. 504 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: 0.44 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 955 1.34 - 1.46: 876 1.46 - 1.58: 1397 1.58 - 1.70: 0 1.70 - 1.81: 35 Bond restraints: 3263 Sorted by residual: bond pdb=" C MET A 35 " pdb=" N PRO A 36 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.19e-02 7.06e+03 1.59e+00 bond pdb=" N MET A 35 " pdb=" CA MET A 35 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.04e-02 9.25e+03 1.13e+00 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.241 1.230 0.011 1.03e-02 9.43e+03 1.08e+00 bond pdb=" CA ARG A 286 " pdb=" C ARG A 286 " ideal model delta sigma weight residual 1.521 1.538 -0.017 1.65e-02 3.67e+03 1.03e+00 bond pdb=" CA LEU A 348 " pdb=" C LEU A 348 " ideal model delta sigma weight residual 1.522 1.509 0.013 1.38e-02 5.25e+03 9.56e-01 ... (remaining 3258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 4289 1.97 - 3.95: 127 3.95 - 5.92: 17 5.92 - 7.89: 5 7.89 - 9.87: 1 Bond angle restraints: 4439 Sorted by residual: angle pdb=" N ALA A 280 " pdb=" CA ALA A 280 " pdb=" C ALA A 280 " ideal model delta sigma weight residual 113.18 106.03 7.15 1.33e+00 5.65e-01 2.89e+01 angle pdb=" N VAL A 275 " pdb=" CA VAL A 275 " pdb=" C VAL A 275 " ideal model delta sigma weight residual 113.22 107.24 5.98 1.23e+00 6.61e-01 2.36e+01 angle pdb=" N LYS A 64 " pdb=" CA LYS A 64 " pdb=" C LYS A 64 " ideal model delta sigma weight residual 114.31 108.06 6.25 1.29e+00 6.01e-01 2.35e+01 angle pdb=" N VAL A 369 " pdb=" CA VAL A 369 " pdb=" C VAL A 369 " ideal model delta sigma weight residual 112.96 108.24 4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" N ASN A 91 " pdb=" CA ASN A 91 " pdb=" C ASN A 91 " ideal model delta sigma weight residual 113.55 108.91 4.64 1.26e+00 6.30e-01 1.35e+01 ... (remaining 4434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 1599 17.77 - 35.54: 213 35.54 - 53.31: 39 53.31 - 71.09: 4 71.09 - 88.86: 2 Dihedral angle restraints: 1857 sinusoidal: 677 harmonic: 1180 Sorted by residual: dihedral pdb=" CA ALA A 279 " pdb=" C ALA A 279 " pdb=" N ALA A 280 " pdb=" CA ALA A 280 " ideal model delta harmonic sigma weight residual 180.00 158.33 21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY A 247 " pdb=" C GLY A 247 " pdb=" N GLN A 248 " pdb=" CA GLN A 248 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASN A 27 " pdb=" C ASN A 27 " pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta harmonic sigma weight residual 180.00 163.55 16.45 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 1854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 248 0.025 - 0.051: 161 0.051 - 0.076: 62 0.076 - 0.101: 23 0.101 - 0.126: 7 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA VAL A 275 " pdb=" N VAL A 275 " pdb=" C VAL A 275 " pdb=" CB VAL A 275 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA ILE A 42 " pdb=" N ILE A 42 " pdb=" C ILE A 42 " pdb=" CB ILE A 42 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA MET A 35 " pdb=" N MET A 35 " pdb=" C MET A 35 " pdb=" CB MET A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 498 not shown) Planarity restraints: 545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 152 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO A 153 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 249 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C PHE A 249 " -0.038 2.00e-02 2.50e+03 pdb=" O PHE A 249 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 250 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 118 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.03e+00 pdb=" N PRO A 119 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.020 5.00e-02 4.00e+02 ... (remaining 542 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 367 2.75 - 3.29: 3102 3.29 - 3.83: 5356 3.83 - 4.36: 6861 4.36 - 4.90: 11390 Nonbonded interactions: 27076 Sorted by model distance: nonbonded pdb=" O LEU A 220 " pdb=" OG SER A 223 " model vdw 2.213 3.040 nonbonded pdb=" OE1 GLU A 41 " pdb=" NE1 TRP A 165 " model vdw 2.258 3.120 nonbonded pdb=" OH TYR A 6 " pdb=" O ARG A 197 " model vdw 2.266 3.040 nonbonded pdb=" O LEU A 382 " pdb=" OG1 THR A 386 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASN A 354 " pdb=" NE2 HIS A 366 " model vdw 2.283 3.120 ... (remaining 27071 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.190 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.003 0.024 3263 Z= 0.181 Angle : 0.836 9.867 4439 Z= 0.562 Chirality : 0.039 0.126 501 Planarity : 0.005 0.059 545 Dihedral : 15.971 88.857 1107 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.30 % Allowed : 23.88 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.97 (0.37), residues: 412 helix: -2.51 (0.25), residues: 332 sheet: None (None), residues: 0 loop : -1.93 (0.62), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 415 TYR 0.010 0.001 TYR A 21 PHE 0.012 0.001 PHE A 51 TRP 0.006 0.001 TRP A 227 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3263) covalent geometry : angle 0.83632 ( 4439) hydrogen bonds : bond 0.23537 ( 169) hydrogen bonds : angle 9.37118 ( 504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.113 Fit side-chains REVERT: A 288 MET cc_start: 0.6885 (tpt) cc_final: 0.6314 (tpt) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.0885 time to fit residues: 4.6261 Evaluate side-chains 43 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.122653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.093626 restraints weight = 3661.653| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.59 r_work: 0.2833 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3263 Z= 0.126 Angle : 0.598 10.618 4439 Z= 0.312 Chirality : 0.038 0.136 501 Planarity : 0.006 0.051 545 Dihedral : 5.518 28.666 443 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.39 % Allowed : 20.00 % Favored : 77.61 % 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: -2.94 (0.39), residues: 412 helix: -1.74 (0.27), residues: 340 sheet: None (None), residues: 0 loop : -1.80 (0.68), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 300 TYR 0.009 0.001 TYR A 225 PHE 0.012 0.001 PHE A 340 TRP 0.006 0.001 TRP A 227 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3263) covalent geometry : angle 0.59781 ( 4439) hydrogen bonds : bond 0.03908 ( 169) hydrogen bonds : angle 5.93257 ( 504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.123 Fit side-chains REVERT: A 251 LEU cc_start: 0.8319 (mt) cc_final: 0.8099 (mt) REVERT: A 418 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7459 (ttp80) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.0857 time to fit residues: 5.1270 Evaluate side-chains 43 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.090506 restraints weight = 3605.251| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.68 r_work: 0.2784 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3263 Z= 0.129 Angle : 0.556 9.453 4439 Z= 0.288 Chirality : 0.037 0.133 501 Planarity : 0.005 0.047 545 Dihedral : 5.236 23.975 443 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.79 % Allowed : 21.49 % Favored : 76.72 % 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: -2.20 (0.40), residues: 412 helix: -1.18 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -1.81 (0.69), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.009 0.001 TYR A 21 PHE 0.012 0.001 PHE A 340 TRP 0.005 0.001 TRP A 227 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3263) covalent geometry : angle 0.55594 ( 4439) hydrogen bonds : bond 0.03357 ( 169) hydrogen bonds : angle 5.41530 ( 504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.112 Fit side-chains REVERT: A 270 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7488 (mm-30) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.0804 time to fit residues: 3.9907 Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.121106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.090664 restraints weight = 3535.787| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.66 r_work: 0.2789 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3263 Z= 0.118 Angle : 0.530 8.531 4439 Z= 0.273 Chirality : 0.037 0.133 501 Planarity : 0.005 0.045 545 Dihedral : 4.933 19.190 442 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.69 % Allowed : 21.49 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.77 (0.41), residues: 412 helix: -0.88 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.72 (0.70), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 418 TYR 0.009 0.001 TYR A 21 PHE 0.012 0.001 PHE A 340 TRP 0.005 0.001 TRP A 227 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3263) covalent geometry : angle 0.53021 ( 4439) hydrogen bonds : bond 0.03096 ( 169) hydrogen bonds : angle 5.19299 ( 504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.070 Fit side-chains REVERT: A 127 LYS cc_start: 0.7938 (mtpm) cc_final: 0.7652 (mtpt) REVERT: A 270 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7516 (mm-30) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 0.0309 time to fit residues: 1.9856 Evaluate side-chains 44 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 385 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.0570 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 19 optimal weight: 0.2980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.123031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.092666 restraints weight = 3523.104| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.64 r_work: 0.2818 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3263 Z= 0.097 Angle : 0.519 12.226 4439 Z= 0.262 Chirality : 0.036 0.125 501 Planarity : 0.005 0.044 545 Dihedral : 4.706 18.317 442 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.49 % Allowed : 22.69 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 412 helix: -0.46 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.76 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 418 TYR 0.008 0.001 TYR A 225 PHE 0.011 0.001 PHE A 340 TRP 0.004 0.001 TRP A 330 HIS 0.000 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 3263) covalent geometry : angle 0.51926 ( 4439) hydrogen bonds : bond 0.02773 ( 169) hydrogen bonds : angle 4.99555 ( 504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.069 Fit side-chains REVERT: A 1 MET cc_start: 0.6470 (tpp) cc_final: 0.6174 (tpp) REVERT: A 24 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 27 ASN cc_start: 0.9023 (m110) cc_final: 0.8464 (m110) REVERT: A 127 LYS cc_start: 0.7820 (mtpm) cc_final: 0.7555 (mtpt) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.0297 time to fit residues: 1.5647 Evaluate side-chains 38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TYR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 0.0970 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.121223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.090539 restraints weight = 3517.487| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.69 r_work: 0.2782 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3263 Z= 0.111 Angle : 0.518 11.095 4439 Z= 0.261 Chirality : 0.037 0.130 501 Planarity : 0.005 0.045 545 Dihedral : 4.621 19.201 442 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.79 % Allowed : 22.09 % Favored : 76.12 % 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: -0.93 (0.42), residues: 412 helix: -0.24 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.75 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.009 0.001 TYR A 21 PHE 0.011 0.001 PHE A 340 TRP 0.004 0.001 TRP A 227 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 3263) covalent geometry : angle 0.51799 ( 4439) hydrogen bonds : bond 0.02869 ( 169) hydrogen bonds : angle 4.93734 ( 504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.118 Fit side-chains REVERT: A 1 MET cc_start: 0.6473 (tpp) cc_final: 0.6168 (tpp) REVERT: A 24 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7895 (t80) REVERT: A 27 ASN cc_start: 0.9076 (m110) cc_final: 0.8464 (m110) REVERT: A 127 LYS cc_start: 0.7768 (mtpm) cc_final: 0.7539 (mtpp) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 0.0457 time to fit residues: 2.4316 Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TYR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 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 = 0.3267 r_free = 0.3267 target = 0.120446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.089476 restraints weight = 3588.763| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.70 r_work: 0.2770 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.003 0.039 3263 Z= 0.118 Angle : 0.519 11.114 4439 Z= 0.261 Chirality : 0.037 0.132 501 Planarity : 0.005 0.045 545 Dihedral : 4.577 19.243 442 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.58 % Allowed : 20.00 % Favored : 76.42 % 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: -0.66 (0.42), residues: 412 helix: -0.06 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.61 (0.74), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.009 0.001 TYR A 21 PHE 0.012 0.001 PHE A 340 TRP 0.005 0.001 TRP A 227 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3263) covalent geometry : angle 0.51943 ( 4439) hydrogen bonds : bond 0.02877 ( 169) hydrogen bonds : angle 4.94445 ( 504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.121 Fit side-chains REVERT: A 1 MET cc_start: 0.6451 (tpp) cc_final: 0.6126 (tpp) REVERT: A 24 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.7839 (t80) REVERT: A 27 ASN cc_start: 0.9098 (m110) cc_final: 0.8429 (m110) REVERT: A 107 TRP cc_start: 0.9075 (OUTLIER) cc_final: 0.8543 (t-100) outliers start: 12 outliers final: 8 residues processed: 38 average time/residue: 0.0315 time to fit residues: 1.6858 Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TYR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.0670 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.121834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.090574 restraints weight = 3626.744| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.74 r_work: 0.2776 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3263 Z= 0.099 Angle : 0.505 10.879 4439 Z= 0.253 Chirality : 0.037 0.125 501 Planarity : 0.005 0.044 545 Dihedral : 4.493 18.657 442 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.99 % Allowed : 20.30 % Favored : 76.72 % 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: -0.40 (0.43), residues: 412 helix: 0.13 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.59 (0.73), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.009 0.001 TYR A 225 PHE 0.011 0.001 PHE A 340 TRP 0.005 0.001 TRP A 393 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 3263) covalent geometry : angle 0.50474 ( 4439) hydrogen bonds : bond 0.02741 ( 169) hydrogen bonds : angle 4.88330 ( 504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.117 Fit side-chains REVERT: A 1 MET cc_start: 0.6470 (tpp) cc_final: 0.6160 (tpp) REVERT: A 24 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7675 (t80) REVERT: A 27 ASN cc_start: 0.9061 (m110) cc_final: 0.8463 (m110) REVERT: A 127 LYS cc_start: 0.7878 (mtpm) cc_final: 0.7609 (mtpp) outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 0.0446 time to fit residues: 2.3815 Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TYR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 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 = 0.3271 r_free = 0.3271 target = 0.120571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.089458 restraints weight = 3599.929| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.69 r_work: 0.2771 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3263 Z= 0.118 Angle : 0.516 10.823 4439 Z= 0.258 Chirality : 0.037 0.129 501 Planarity : 0.005 0.045 545 Dihedral : 4.495 19.325 442 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.99 % Allowed : 20.30 % Favored : 76.72 % 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: -0.26 (0.42), residues: 412 helix: 0.23 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.54 (0.73), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.009 0.001 TYR A 21 PHE 0.011 0.001 PHE A 340 TRP 0.005 0.001 TRP A 227 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3263) covalent geometry : angle 0.51581 ( 4439) hydrogen bonds : bond 0.02866 ( 169) hydrogen bonds : angle 4.89504 ( 504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.124 Fit side-chains REVERT: A 1 MET cc_start: 0.6450 (tpp) cc_final: 0.6170 (tpp) REVERT: A 24 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.7690 (t80) REVERT: A 27 ASN cc_start: 0.9085 (m110) cc_final: 0.8399 (m110) outliers start: 10 outliers final: 9 residues processed: 38 average time/residue: 0.0381 time to fit residues: 2.1308 Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TYR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.120526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.089319 restraints weight = 3546.378| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.68 r_work: 0.2763 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3263 Z= 0.113 Angle : 0.512 10.742 4439 Z= 0.256 Chirality : 0.037 0.127 501 Planarity : 0.005 0.045 545 Dihedral : 4.470 19.108 442 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.99 % Allowed : 20.60 % Favored : 76.42 % 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: -0.04 (0.42), residues: 412 helix: 0.39 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.52 (0.73), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.009 0.001 TYR A 225 PHE 0.011 0.001 PHE A 340 TRP 0.005 0.001 TRP A 227 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3263) covalent geometry : angle 0.51237 ( 4439) hydrogen bonds : bond 0.02830 ( 169) hydrogen bonds : angle 4.89044 ( 504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.112 Fit side-chains REVERT: A 1 MET cc_start: 0.6471 (tpp) cc_final: 0.6241 (tpp) REVERT: A 24 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 27 ASN cc_start: 0.9079 (m110) cc_final: 0.8405 (m110) outliers start: 10 outliers final: 9 residues processed: 36 average time/residue: 0.0307 time to fit residues: 1.6589 Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TYR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.0570 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.123535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.093300 restraints weight = 3597.404| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.59 r_work: 0.2828 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3263 Z= 0.091 Angle : 0.495 10.824 4439 Z= 0.247 Chirality : 0.036 0.121 501 Planarity : 0.004 0.044 545 Dihedral : 4.365 18.103 442 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.99 % Allowed : 20.60 % Favored : 76.42 % 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: 0.32 (0.43), residues: 412 helix: 0.64 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.42 (0.75), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.009 0.001 TYR A 225 PHE 0.010 0.001 PHE A 340 TRP 0.007 0.001 TRP A 393 HIS 0.000 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 3263) covalent geometry : angle 0.49462 ( 4439) hydrogen bonds : bond 0.02586 ( 169) hydrogen bonds : angle 4.79202 ( 504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 988.87 seconds wall clock time: 17 minutes 35.72 seconds (1055.72 seconds total)