Starting phenix.real_space_refine on Thu Sep 10 21:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uwf_20922/09_2026/6uwf_20922.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uwf_20922/09_2026/6uwf_20922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6uwf_20922/09_2026/6uwf_20922.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uwf_20922/09_2026/6uwf_20922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uwf_20922/09_2026/6uwf_20922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uwf_20922/09_2026/6uwf_20922.map" model { file = "/net/cci-nas-00/data/ceres_data/6uwf_20922/09_2026/6uwf_20922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uwf_20922/09_2026/6uwf_20922.cif" } resolution = 3.08 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= 0.002 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 2 5.49 5 S 18 5.16 5 C 2096 2.51 5 N 502 2.21 5 O 560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 3178 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3105 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 0.88, per 1000 atoms: 0.28 Number of scatterers: 3178 At special positions: 0 Unit cell: (71.02, 67.84, 81.62, 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 2 15.00 O 560 8.00 N 502 7.00 C 2096 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 93.6 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 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: 20 helices and 0 sheets defined 84.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.650A pdb=" N LYS A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.883A pdb=" N VAL A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.982A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.589A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 107 removed outlier: 3.630A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.619A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.586A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.737A pdb=" N ARG A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.617A pdb=" N TYR A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.528A pdb=" N LYS A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 257 through 276 removed outlier: 5.780A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 295 through 307 removed outlier: 4.264A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 311 through 329 removed outlier: 3.545A pdb=" N THR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.725A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.790A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.818A pdb=" N ALA A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 416 removed outlier: 4.063A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 672 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: 0.53 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 488 1.31 - 1.43: 788 1.43 - 1.56: 1894 1.56 - 1.68: 31 1.68 - 1.80: 35 Bond restraints: 3236 Sorted by residual: bond pdb=" C16 6OU A 502 " pdb=" O18 6OU A 502 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C16 6OU A 503 " pdb=" O18 6OU A 503 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C31 6OU A 502 " pdb=" O30 6OU A 502 " ideal model delta sigma weight residual 1.331 1.410 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C31 6OU A 503 " pdb=" O30 6OU A 503 " ideal model delta sigma weight residual 1.331 1.409 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C39 6OU A 502 " pdb=" C40 6OU A 502 " ideal model delta sigma weight residual 1.497 1.569 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 3231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 4295 3.07 - 6.14: 80 6.14 - 9.21: 15 9.21 - 12.28: 2 12.28 - 15.35: 2 Bond angle restraints: 4394 Sorted by residual: angle pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " pdb=" O26 6OU A 502 " ideal model delta sigma weight residual 93.95 109.30 -15.35 3.00e+00 1.11e-01 2.62e+01 angle pdb=" O22 6OU A 503 " pdb=" P23 6OU A 503 " pdb=" O26 6OU A 503 " ideal model delta sigma weight residual 93.95 108.18 -14.23 3.00e+00 1.11e-01 2.25e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 118.33 -8.52 2.21e+00 2.05e-01 1.48e+01 angle pdb=" N LEU A 374 " pdb=" CA LEU A 374 " pdb=" C LEU A 374 " ideal model delta sigma weight residual 113.17 108.81 4.36 1.26e+00 6.30e-01 1.20e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 119.66 -5.76 1.80e+00 3.09e-01 1.03e+01 ... (remaining 4389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 1831 28.42 - 56.85: 60 56.85 - 85.27: 8 85.27 - 113.70: 1 113.70 - 142.12: 3 Dihedral angle restraints: 1903 sinusoidal: 720 harmonic: 1183 Sorted by residual: dihedral pdb=" CA GLN A 121 " pdb=" C GLN A 121 " pdb=" N PHE A 122 " pdb=" CA PHE A 122 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" C37 6OU A 503 " pdb=" C38 6OU A 503 " pdb=" C39 6OU A 503 " pdb=" C40 6OU A 503 " ideal model delta sinusoidal sigma weight residual 178.01 -39.87 -142.12 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C09 6OU A 503 " pdb=" C10 6OU A 503 " pdb=" C11 6OU A 503 " pdb=" C12 6OU A 503 " ideal model delta sinusoidal sigma weight residual 179.71 -48.47 -131.82 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 1900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 368 0.046 - 0.092: 134 0.092 - 0.137: 29 0.137 - 0.183: 7 0.183 - 0.229: 3 Chirality restraints: 541 Sorted by residual: chirality pdb=" CA SER A 74 " pdb=" N SER A 74 " pdb=" C SER A 74 " pdb=" CB SER A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C20 6OU A 503 " pdb=" C19 6OU A 503 " pdb=" C21 6OU A 503 " pdb=" O30 6OU A 503 " both_signs ideal model delta sigma weight residual False 2.35 2.56 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL A 117 " pdb=" CA VAL A 117 " pdb=" CG1 VAL A 117 " pdb=" CG2 VAL A 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.82 0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 538 not shown) Planarity restraints: 537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 45 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 152 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 153 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 206 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.030 5.00e-02 4.00e+02 ... (remaining 534 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 910 2.82 - 3.34: 3006 3.34 - 3.86: 5315 3.86 - 4.38: 6264 4.38 - 4.90: 10738 Nonbonded interactions: 26233 Sorted by model distance: nonbonded pdb=" O ALA A 360 " pdb=" OH TYR A 383 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.321 3.040 nonbonded pdb=" O GLU A 296 " pdb=" OG SER A 300 " model vdw 2.325 3.040 nonbonded pdb=" O THR A 340 " pdb=" OG1 THR A 344 " model vdw 2.336 3.040 nonbonded pdb=" O ALA A 348 " pdb=" OG1 THR A 352 " model vdw 2.345 3.040 ... (remaining 26228 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: 1.270 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: 0.000 Set scattering table: 0.010 Process input model: 4.490 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 : 0.008 0.088 3237 Z= 0.376 Angle : 1.079 15.348 4394 Z= 0.513 Chirality : 0.049 0.229 541 Planarity : 0.008 0.054 537 Dihedral : 16.397 142.124 1153 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.32), residues: 413 helix: -2.35 (0.20), residues: 338 sheet: None (None), residues: 0 loop : -2.27 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 287 TYR 0.029 0.003 TYR A 299 PHE 0.015 0.002 PHE A 157 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00791 / 0.38 ( 3236) covalent geometry : angle 1.07857 / 0.51 ( 4394) hydrogen bonds : bond 0.11687 / 6.33 ( 224) hydrogen bonds : angle 5.88084 / 4.06 ( 672) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.092 Fit side-chains REVERT: A 327 ASN cc_start: 0.8784 (m110) cc_final: 0.8305 (m-40) REVERT: A 362 MET cc_start: 0.9011 (tpp) cc_final: 0.8494 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0355 time to fit residues: 2.3675 Evaluate side-chains 41 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.091548 restraints weight = 4431.656| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.62 r_work: 0.2797 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3237 Z= 0.167 Angle : 0.595 5.865 4394 Z= 0.301 Chirality : 0.040 0.147 541 Planarity : 0.005 0.034 537 Dihedral : 14.102 126.454 489 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.31 % Allowed : 10.15 % Favored : 89.54 % 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: -1.37 (0.38), residues: 413 helix: -0.49 (0.26), residues: 343 sheet: None (None), residues: 0 loop : -2.30 (0.66), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 287 TYR 0.024 0.002 TYR A 299 PHE 0.010 0.001 PHE A 157 HIS 0.002 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 3236) covalent geometry : angle 0.59489 / 0.30 ( 4394) hydrogen bonds : bond 0.04606 / 2.91 ( 224) hydrogen bonds : angle 4.68574 / 3.21 ( 672) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.129 Fit side-chains REVERT: A 327 ASN cc_start: 0.8918 (m110) cc_final: 0.8291 (m-40) REVERT: A 362 MET cc_start: 0.9314 (tpp) cc_final: 0.8785 (tpt) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.0411 time to fit residues: 2.6758 Evaluate side-chains 42 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.114888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.093245 restraints weight = 4282.288| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.69 r_work: 0.2741 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3237 Z= 0.117 Angle : 0.530 5.633 4394 Z= 0.265 Chirality : 0.038 0.142 541 Planarity : 0.004 0.030 537 Dihedral : 13.041 114.803 489 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.23 % Allowed : 10.77 % Favored : 88.00 % 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: 0.03 (0.41), residues: 413 helix: 0.52 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -2.14 (0.66), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.018 0.001 TYR A 299 PHE 0.008 0.001 PHE A 157 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 3236) covalent geometry : angle 0.53000 / 0.27 ( 4394) hydrogen bonds : bond 0.03833 / 2.43 ( 224) hydrogen bonds : angle 4.40061 / 3.02 ( 672) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.119 Fit side-chains REVERT: A 61 ILE cc_start: 0.8770 (tt) cc_final: 0.8551 (tt) REVERT: A 219 GLU cc_start: 0.7857 (tt0) cc_final: 0.7519 (mt-10) REVERT: A 327 ASN cc_start: 0.8616 (m110) cc_final: 0.8002 (m-40) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 0.0390 time to fit residues: 2.5026 Evaluate side-chains 44 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 312 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3269 r_free = 0.3269 target = 0.111840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.089816 restraints weight = 4278.172| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.69 r_work: 0.2753 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3237 Z= 0.148 Angle : 0.557 5.403 4394 Z= 0.278 Chirality : 0.039 0.140 541 Planarity : 0.004 0.030 537 Dihedral : 12.799 106.830 489 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.85 % Allowed : 12.31 % Favored : 85.85 % 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: 0.63 (0.42), residues: 413 helix: 1.00 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -2.12 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 287 TYR 0.019 0.001 TYR A 299 PHE 0.010 0.001 PHE A 157 HIS 0.002 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 3236) covalent geometry : angle 0.55721 / 0.28 ( 4394) hydrogen bonds : bond 0.04094 / 2.60 ( 224) hydrogen bonds : angle 4.42742 / 3.04 ( 672) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.113 Fit side-chains REVERT: A 61 ILE cc_start: 0.8890 (tt) cc_final: 0.8688 (tt) REVERT: A 327 ASN cc_start: 0.8693 (m110) cc_final: 0.8080 (m-40) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.0364 time to fit residues: 2.4427 Evaluate side-chains 47 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.0670 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 0.0030 overall best weight: 0.1724 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.117656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.095854 restraints weight = 4231.978| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.69 r_work: 0.2780 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3237 Z= 0.100 Angle : 0.507 5.652 4394 Z= 0.251 Chirality : 0.037 0.130 541 Planarity : 0.004 0.028 537 Dihedral : 12.051 90.897 489 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: 1.35 (0.42), residues: 413 helix: 1.39 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.56 (0.73), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.015 0.001 TYR A 299 PHE 0.008 0.001 PHE A 157 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 3236) covalent geometry : angle 0.50732 / 0.25 ( 4394) hydrogen bonds : bond 0.03355 / 2.14 ( 224) hydrogen bonds : angle 4.13303 / 2.85 ( 672) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.111 Fit side-chains REVERT: A 61 ILE cc_start: 0.8786 (tt) cc_final: 0.8572 (tt) REVERT: A 219 GLU cc_start: 0.7870 (tt0) cc_final: 0.7556 (mt-10) REVERT: A 327 ASN cc_start: 0.8532 (m110) cc_final: 0.8010 (m-40) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.0361 time to fit residues: 2.2777 Evaluate side-chains 43 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 11 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 0.0870 chunk 1 optimal weight: 0.0980 overall best weight: 0.2558 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.117094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.095331 restraints weight = 4142.346| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.67 r_work: 0.2774 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3237 Z= 0.104 Angle : 0.513 7.025 4394 Z= 0.251 Chirality : 0.037 0.131 541 Planarity : 0.004 0.028 537 Dihedral : 11.706 89.987 489 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.85 % Allowed : 13.85 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.43), residues: 413 helix: 1.71 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.76 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.017 0.001 TYR A 299 PHE 0.009 0.001 PHE A 157 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 3236) covalent geometry : angle 0.51277 / 0.25 ( 4394) hydrogen bonds : bond 0.03422 / 2.19 ( 224) hydrogen bonds : angle 4.12551 / 2.83 ( 672) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.116 Fit side-chains REVERT: A 61 ILE cc_start: 0.8784 (tt) cc_final: 0.8549 (tt) REVERT: A 219 GLU cc_start: 0.7775 (tt0) cc_final: 0.7408 (mt-10) REVERT: A 327 ASN cc_start: 0.8514 (m110) cc_final: 0.8012 (m-40) outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.0365 time to fit residues: 2.4193 Evaluate side-chains 45 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 0.3098 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.116934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.094907 restraints weight = 4291.315| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.69 r_work: 0.2765 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3237 Z= 0.110 Angle : 0.520 8.021 4394 Z= 0.255 Chirality : 0.038 0.136 541 Planarity : 0.004 0.029 537 Dihedral : 11.489 89.182 489 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.54 % Allowed : 14.46 % 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: 1.83 (0.43), residues: 413 helix: 1.74 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -1.49 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.017 0.001 TYR A 299 PHE 0.008 0.001 PHE A 157 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 3236) covalent geometry : angle 0.51958 / 0.26 ( 4394) hydrogen bonds : bond 0.03456 / 2.21 ( 224) hydrogen bonds : angle 4.11967 / 2.83 ( 672) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.111 Fit side-chains REVERT: A 61 ILE cc_start: 0.8797 (tt) cc_final: 0.8564 (tt) REVERT: A 219 GLU cc_start: 0.7810 (tt0) cc_final: 0.7550 (mt-10) REVERT: A 327 ASN cc_start: 0.8512 (m110) cc_final: 0.8007 (m-40) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.0367 time to fit residues: 2.3282 Evaluate side-chains 46 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.0170 chunk 25 optimal weight: 0.0770 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.114700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092643 restraints weight = 4323.839| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.70 r_work: 0.2730 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3237 Z= 0.138 Angle : 0.551 9.054 4394 Z= 0.268 Chirality : 0.039 0.134 541 Planarity : 0.004 0.028 537 Dihedral : 11.446 84.345 489 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.54 % Allowed : 14.46 % 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: 1.74 (0.43), residues: 413 helix: 1.76 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.71 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.018 0.001 TYR A 299 PHE 0.010 0.001 PHE A 157 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 3236) covalent geometry : angle 0.55085 / 0.27 ( 4394) hydrogen bonds : bond 0.03830 / 2.44 ( 224) hydrogen bonds : angle 4.22873 / 2.89 ( 672) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.080 Fit side-chains REVERT: A 61 ILE cc_start: 0.8827 (tt) cc_final: 0.8611 (tt) REVERT: A 219 GLU cc_start: 0.7796 (tt0) cc_final: 0.7436 (mt-10) REVERT: A 327 ASN cc_start: 0.8570 (m110) cc_final: 0.8044 (m-40) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.0323 time to fit residues: 2.0418 Evaluate side-chains 46 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.113444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.092392 restraints weight = 4367.042| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.62 r_work: 0.2841 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3237 Z= 0.138 Angle : 0.555 9.406 4394 Z= 0.270 Chirality : 0.039 0.132 541 Planarity : 0.004 0.028 537 Dihedral : 11.337 78.259 489 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.15 % Allowed : 13.85 % 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: 1.71 (0.43), residues: 413 helix: 1.74 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.71 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.018 0.001 TYR A 299 PHE 0.009 0.001 PHE A 157 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 3236) covalent geometry : angle 0.55460 / 0.27 ( 4394) hydrogen bonds : bond 0.03859 / 2.46 ( 224) hydrogen bonds : angle 4.24155 / 2.90 ( 672) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.068 Fit side-chains REVERT: A 327 ASN cc_start: 0.8857 (m110) cc_final: 0.8363 (m-40) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.0301 time to fit residues: 1.9955 Evaluate side-chains 48 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.0170 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 20 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.116661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.095542 restraints weight = 4349.579| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.63 r_work: 0.2841 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3237 Z= 0.118 Angle : 0.542 9.806 4394 Z= 0.263 Chirality : 0.039 0.132 541 Planarity : 0.004 0.028 537 Dihedral : 11.080 75.318 489 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.85 % Allowed : 13.85 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.43), residues: 413 helix: 1.76 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -1.44 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.017 0.001 TYR A 299 PHE 0.008 0.001 PHE A 157 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 3236) covalent geometry : angle 0.54232 / 0.26 ( 4394) hydrogen bonds : bond 0.03663 / 2.33 ( 224) hydrogen bonds : angle 4.19233 / 2.87 ( 672) Misc. bond : bond 0.00007 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8846 (m110) cc_final: 0.8366 (m-40) outliers start: 6 outliers final: 6 residues processed: 45 average time/residue: 0.0323 time to fit residues: 2.1164 Evaluate side-chains 49 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 37 optimal weight: 0.1980 chunk 5 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 overall best weight: 0.2378 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.117574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095441 restraints weight = 4277.140| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.71 r_work: 0.2784 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.002 0.024 3237 Z= 0.103 Angle : 0.533 10.332 4394 Z= 0.259 Chirality : 0.038 0.128 541 Planarity : 0.004 0.028 537 Dihedral : 10.614 70.404 489 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.54 % Allowed : 14.46 % 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: 2.02 (0.43), residues: 413 helix: 1.87 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -1.40 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.017 0.001 TYR A 299 PHE 0.008 0.001 PHE A 157 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 3236) covalent geometry : angle 0.53286 / 0.26 ( 4394) hydrogen bonds : bond 0.03325 / 2.12 ( 224) hydrogen bonds : angle 4.08739 / 2.81 ( 672) Misc. bond : bond 0.00002 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 943.23 seconds wall clock time: 16 minutes 49.53 seconds (1009.53 seconds total)