Starting phenix.real_space_refine on Wed Jul 1 22:12:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xq2_33389/07_2026/7xq2_33389_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xq2_33389/07_2026/7xq2_33389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xq2_33389/07_2026/7xq2_33389_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xq2_33389/07_2026/7xq2_33389_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xq2_33389/07_2026/7xq2_33389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xq2_33389/07_2026/7xq2_33389.map" } resolution = 3.3 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= 0.004 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 4 5.49 5 S 10 5.16 5 C 2222 2.51 5 N 565 2.21 5 O 576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3377 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3287 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain breaks: 1 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'1SY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.78, per 1000 atoms: 0.23 Number of scatterers: 3377 At special positions: 0 Unit cell: (80, 75, 67, 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 10 16.00 P 4 15.00 O 576 8.00 N 565 7.00 C 2222 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: 0.16 Conformation dependent library (CDL) restraints added in 85.9 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 81.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.727A pdb=" N TRP A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.831A pdb=" N GLN A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.567A pdb=" N THR A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.767A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.751A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.565A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 132 removed outlier: 3.616A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.979A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.789A pdb=" N TYR A 149 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 176 removed outlier: 3.502A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.946A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 264 through 296 removed outlier: 3.601A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 removed outlier: 3.940A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 removed outlier: 4.290A pdb=" N VAL A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 356 removed outlier: 3.729A pdb=" N ALA A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 388 removed outlier: 3.791A pdb=" N CYS A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 418 removed outlier: 3.778A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 455 removed outlier: 3.691A pdb=" N GLN A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 609 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: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 470 1.31 - 1.44: 1079 1.44 - 1.56: 1905 1.56 - 1.68: 1 1.68 - 1.80: 24 Bond restraints: 3479 Sorted by residual: bond pdb=" C36 1SY A 601 " pdb=" N42 1SY A 601 " ideal model delta sigma weight residual 1.357 1.496 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C36 1SY A 602 " pdb=" N42 1SY A 602 " ideal model delta sigma weight residual 1.357 1.495 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C40 1SY A 601 " pdb=" N39 1SY A 601 " ideal model delta sigma weight residual 1.304 1.441 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C40 1SY A 602 " pdb=" N39 1SY A 602 " ideal model delta sigma weight residual 1.304 1.439 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C21 1SY A 601 " pdb=" C32 1SY A 601 " ideal model delta sigma weight residual 1.533 1.411 0.122 2.00e-02 2.50e+03 3.70e+01 ... (remaining 3474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 4665 3.73 - 7.45: 66 7.45 - 11.18: 17 11.18 - 14.90: 9 14.90 - 18.63: 4 Bond angle restraints: 4761 Sorted by residual: angle pdb=" O19 1SY A 602 " pdb=" P18 1SY A 602 " pdb=" O44 1SY A 602 " ideal model delta sigma weight residual 123.21 104.58 18.63 3.00e+00 1.11e-01 3.86e+01 angle pdb=" O19 1SY A 601 " pdb=" P18 1SY A 601 " pdb=" O44 1SY A 601 " ideal model delta sigma weight residual 123.21 105.02 18.19 3.00e+00 1.11e-01 3.68e+01 angle pdb=" O29 1SY A 601 " pdb=" P27 1SY A 601 " pdb=" O30 1SY A 601 " ideal model delta sigma weight residual 123.47 106.66 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" O29 1SY A 602 " pdb=" P27 1SY A 602 " pdb=" O30 1SY A 602 " ideal model delta sigma weight residual 123.47 107.14 16.33 3.00e+00 1.11e-01 2.96e+01 angle pdb=" N ARG A 330 " pdb=" CA ARG A 330 " pdb=" C ARG A 330 " ideal model delta sigma weight residual 111.69 118.11 -6.42 1.23e+00 6.61e-01 2.73e+01 ... (remaining 4756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 1978 26.67 - 53.35: 76 53.35 - 80.02: 9 80.02 - 106.69: 7 106.69 - 133.36: 7 Dihedral angle restraints: 2077 sinusoidal: 873 harmonic: 1204 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASN A 300 " pdb=" C ASN A 300 " pdb=" N SER A 301 " pdb=" CA SER A 301 " ideal model delta harmonic sigma weight residual 180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" C16 1SY A 601 " pdb=" O17 1SY A 601 " pdb=" P18 1SY A 601 " pdb=" O19 1SY A 601 " ideal model delta sinusoidal sigma weight residual 174.67 -51.97 -133.36 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 2074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 488 0.070 - 0.141: 52 0.141 - 0.211: 7 0.211 - 0.281: 2 0.281 - 0.351: 2 Chirality restraints: 551 Sorted by residual: chirality pdb=" C2' 1SY A 601 " pdb=" C1' 1SY A 601 " pdb=" C3' 1SY A 601 " pdb=" O2' 1SY A 601 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA LYS A 328 " pdb=" N LYS A 328 " pdb=" C LYS A 328 " pdb=" CB LYS A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C2' 1SY A 602 " pdb=" C1' 1SY A 602 " pdb=" C3' 1SY A 602 " pdb=" O2' 1SY A 602 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 548 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 325 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C GLY A 325 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY A 325 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE A 326 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.043 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO A 70 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 49 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO A 50 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " 0.032 5.00e-02 4.00e+02 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 863 2.77 - 3.31: 2940 3.31 - 3.84: 5756 3.84 - 4.37: 7002 4.37 - 4.90: 11986 Nonbonded interactions: 28547 Sorted by model distance: nonbonded pdb=" OH TYR A 149 " pdb=" O30 1SY A 601 " model vdw 2.244 3.040 nonbonded pdb=" O VAL A 64 " pdb=" OG1 THR A 69 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR A 139 " pdb=" O LYS A 204 " model vdw 2.280 3.040 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.294 3.040 nonbonded pdb=" O LYS A 411 " pdb=" OG1 THR A 415 " model vdw 2.300 3.040 ... (remaining 28542 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.750 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.012 0.139 3479 Z= 0.583 Angle : 1.295 18.629 4761 Z= 0.563 Chirality : 0.055 0.351 551 Planarity : 0.006 0.064 564 Dihedral : 17.681 133.365 1303 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.85 % Allowed : 9.92 % Favored : 89.24 % Cbeta Deviations : 0.26 % 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: -6.96 (0.20), residues: 405 helix: -4.57 (0.10), residues: 319 sheet: None (None), residues: 0 loop : -3.38 (0.50), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 157 TYR 0.013 0.002 TYR A 92 PHE 0.009 0.001 PHE A 37 TRP 0.010 0.001 TRP A 107 HIS 0.002 0.000 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.01189 / 0.58 ( 3479) covalent geometry : angle 1.29478 / 0.56 ( 4761) hydrogen bonds : bond 0.28994 / 19.29 ( 204) hydrogen bonds : angle 11.55518 / 8.08 ( 609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.066 Fit side-chains REVERT: A 40 GLN cc_start: 0.7697 (mp10) cc_final: 0.7447 (mp10) REVERT: A 105 SER cc_start: 0.8888 (t) cc_final: 0.8686 (t) REVERT: A 282 TYR cc_start: 0.8284 (m-80) cc_final: 0.7812 (m-80) REVERT: A 364 LEU cc_start: 0.8774 (tp) cc_final: 0.8563 (tt) REVERT: A 371 LEU cc_start: 0.8649 (mm) cc_final: 0.8371 (mt) REVERT: A 430 LYS cc_start: 0.8303 (ttpt) cc_final: 0.8012 (tptt) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.0935 time to fit residues: 5.3580 Evaluate side-chains 40 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.0060 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 289 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.090352 restraints weight = 4058.518| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.68 r_work: 0.2782 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3479 Z= 0.154 Angle : 0.605 7.888 4761 Z= 0.311 Chirality : 0.039 0.116 551 Planarity : 0.005 0.044 564 Dihedral : 8.608 40.860 593 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.28 % Allowed : 11.05 % Favored : 88.67 % 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: -3.53 (0.33), residues: 405 helix: -2.12 (0.23), residues: 317 sheet: None (None), residues: 0 loop : -2.32 (0.56), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.016 0.001 TYR A 35 PHE 0.008 0.001 PHE A 192 TRP 0.014 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 3479) covalent geometry : angle 0.60542 / 0.31 ( 4761) hydrogen bonds : bond 0.03978 / 2.63 ( 204) hydrogen bonds : angle 4.96433 / 3.50 ( 609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.093 Fit side-chains REVERT: A 62 GLU cc_start: 0.7658 (mp0) cc_final: 0.7432 (mp0) REVERT: A 213 ASN cc_start: 0.8606 (m-40) cc_final: 0.8243 (m-40) REVERT: A 254 MET cc_start: 0.7830 (ttp) cc_final: 0.7613 (mtp) REVERT: A 277 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8118 (t0) REVERT: A 303 ARG cc_start: 0.7574 (ttt-90) cc_final: 0.6921 (mtp85) REVERT: A 430 LYS cc_start: 0.8438 (ttpt) cc_final: 0.7275 (tptt) REVERT: A 456 ARG cc_start: 0.7025 (ttt180) cc_final: 0.6027 (tpm170) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.0687 time to fit residues: 3.3911 Evaluate side-chains 38 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.109705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.089911 restraints weight = 4064.371| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.77 r_work: 0.2774 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3479 Z= 0.131 Angle : 0.525 5.912 4761 Z= 0.272 Chirality : 0.038 0.107 551 Planarity : 0.004 0.038 564 Dihedral : 6.117 26.917 588 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.85 % Allowed : 11.05 % Favored : 88.10 % 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: -1.68 (0.38), residues: 405 helix: -0.72 (0.26), residues: 325 sheet: None (None), residues: 0 loop : -2.11 (0.62), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.014 0.001 TYR A 35 PHE 0.008 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 3479) covalent geometry : angle 0.52511 / 0.27 ( 4761) hydrogen bonds : bond 0.03706 / 2.46 ( 204) hydrogen bonds : angle 4.34804 / 3.06 ( 609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.098 Fit side-chains REVERT: A 38 MET cc_start: 0.8704 (mmm) cc_final: 0.8330 (mmm) REVERT: A 254 MET cc_start: 0.7818 (ttp) cc_final: 0.7570 (mtp) REVERT: A 277 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8087 (t0) REVERT: A 303 ARG cc_start: 0.7538 (ttt-90) cc_final: 0.6901 (mtp85) REVERT: A 430 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7110 (tptt) REVERT: A 456 ARG cc_start: 0.6997 (ttt180) cc_final: 0.5975 (tpm170) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.0784 time to fit residues: 3.3105 Evaluate side-chains 36 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 277 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.090303 restraints weight = 3962.539| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.66 r_work: 0.2780 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3479 Z= 0.129 Angle : 0.503 5.412 4761 Z= 0.261 Chirality : 0.038 0.106 551 Planarity : 0.003 0.034 564 Dihedral : 5.660 23.903 588 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.85 % Allowed : 11.33 % Favored : 87.82 % 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: -0.67 (0.41), residues: 405 helix: 0.00 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -1.90 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.013 0.001 TYR A 35 PHE 0.008 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 3479) covalent geometry : angle 0.50283 / 0.26 ( 4761) hydrogen bonds : bond 0.03549 / 2.34 ( 204) hydrogen bonds : angle 4.12385 / 2.90 ( 609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.108 Fit side-chains REVERT: A 38 MET cc_start: 0.8690 (mmm) cc_final: 0.8320 (mmm) REVERT: A 88 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7908 (t0) REVERT: A 254 MET cc_start: 0.7848 (ttp) cc_final: 0.7598 (mtp) REVERT: A 277 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8049 (t0) REVERT: A 303 ARG cc_start: 0.7753 (ttt-90) cc_final: 0.7103 (mtp85) REVERT: A 430 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7106 (tptt) REVERT: A 456 ARG cc_start: 0.7049 (ttt180) cc_final: 0.5966 (tpm170) outliers start: 3 outliers final: 1 residues processed: 41 average time/residue: 0.0852 time to fit residues: 4.0479 Evaluate side-chains 41 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 277 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 7 optimal weight: 0.0470 chunk 13 optimal weight: 0.5980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.109711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.089954 restraints weight = 4033.778| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.69 r_work: 0.2774 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3479 Z= 0.131 Angle : 0.496 5.385 4761 Z= 0.257 Chirality : 0.037 0.111 551 Planarity : 0.003 0.032 564 Dihedral : 5.476 21.990 588 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.13 % Allowed : 11.33 % Favored : 87.54 % 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: -0.18 (0.41), residues: 405 helix: 0.36 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.83 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 333 TYR 0.013 0.001 TYR A 35 PHE 0.008 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 3479) covalent geometry : angle 0.49598 / 0.26 ( 4761) hydrogen bonds : bond 0.03524 / 2.32 ( 204) hydrogen bonds : angle 4.01991 / 2.81 ( 609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.066 Fit side-chains REVERT: A 88 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7933 (t0) REVERT: A 254 MET cc_start: 0.7904 (ttp) cc_final: 0.7651 (mtp) REVERT: A 303 ARG cc_start: 0.7807 (ttt-90) cc_final: 0.7154 (mtp85) REVERT: A 430 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7120 (tptt) REVERT: A 456 ARG cc_start: 0.7031 (ttt180) cc_final: 0.5959 (tpm170) outliers start: 4 outliers final: 1 residues processed: 38 average time/residue: 0.0699 time to fit residues: 3.1752 Evaluate side-chains 36 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.109081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.089459 restraints weight = 4030.067| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.66 r_work: 0.2765 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3479 Z= 0.139 Angle : 0.500 5.385 4761 Z= 0.258 Chirality : 0.038 0.115 551 Planarity : 0.003 0.031 564 Dihedral : 5.356 22.002 588 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.85 % Allowed : 11.90 % Favored : 87.25 % 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: 0.14 (0.42), residues: 405 helix: 0.60 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.79 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.013 0.001 TYR A 35 PHE 0.008 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 3479) covalent geometry : angle 0.49968 / 0.26 ( 4761) hydrogen bonds : bond 0.03538 / 2.33 ( 204) hydrogen bonds : angle 4.00232 / 2.80 ( 609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.108 Fit side-chains REVERT: A 250 VAL cc_start: 0.6205 (OUTLIER) cc_final: 0.5834 (p) REVERT: A 254 MET cc_start: 0.7930 (ttp) cc_final: 0.7659 (mtp) REVERT: A 303 ARG cc_start: 0.7875 (ttt-90) cc_final: 0.7232 (mtp85) REVERT: A 430 LYS cc_start: 0.8414 (ttpt) cc_final: 0.7221 (tptt) REVERT: A 456 ARG cc_start: 0.7044 (ttt180) cc_final: 0.5981 (tpm170) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.0863 time to fit residues: 3.8109 Evaluate side-chains 36 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3134 r_free = 0.3134 target = 0.109055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.089356 restraints weight = 4053.721| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.68 r_work: 0.2760 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3479 Z= 0.144 Angle : 0.503 5.386 4761 Z= 0.260 Chirality : 0.038 0.116 551 Planarity : 0.003 0.030 564 Dihedral : 5.271 21.920 588 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.13 % Allowed : 11.90 % Favored : 86.97 % 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: 0.35 (0.42), residues: 405 helix: 0.74 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.71 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.013 0.001 TYR A 35 PHE 0.008 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 3479) covalent geometry : angle 0.50265 / 0.26 ( 4761) hydrogen bonds : bond 0.03560 / 2.35 ( 204) hydrogen bonds : angle 3.99781 / 2.79 ( 609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.080 Fit side-chains REVERT: A 88 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7892 (t0) REVERT: A 207 LYS cc_start: 0.9022 (mmtp) cc_final: 0.8711 (mmtt) REVERT: A 250 VAL cc_start: 0.6127 (OUTLIER) cc_final: 0.5784 (p) REVERT: A 254 MET cc_start: 0.7865 (ttp) cc_final: 0.7596 (mtp) REVERT: A 303 ARG cc_start: 0.7839 (ttt-90) cc_final: 0.7194 (mtp85) REVERT: A 430 LYS cc_start: 0.8377 (ttpt) cc_final: 0.7167 (tptt) REVERT: A 456 ARG cc_start: 0.7010 (ttt180) cc_final: 0.5936 (tpm170) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.0757 time to fit residues: 3.6233 Evaluate side-chains 41 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.0040 chunk 26 optimal weight: 0.2980 chunk 30 optimal weight: 0.0980 chunk 3 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.2392 ------------------------------------------------------------------------------- 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 = 0.3188 r_free = 0.3188 target = 0.113012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.093492 restraints weight = 3996.599| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.65 r_work: 0.2813 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3479 Z= 0.103 Angle : 0.468 5.349 4761 Z= 0.243 Chirality : 0.036 0.103 551 Planarity : 0.003 0.030 564 Dihedral : 5.034 23.102 588 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.13 % Allowed : 12.75 % Favored : 86.12 % 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: 0.71 (0.43), residues: 405 helix: 1.01 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.66 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.010 0.001 TYR A 35 PHE 0.008 0.001 PHE A 372 TRP 0.014 0.001 TRP A 331 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 3479) covalent geometry : angle 0.46808 / 0.24 ( 4761) hydrogen bonds : bond 0.03287 / 2.15 ( 204) hydrogen bonds : angle 3.81964 / 2.67 ( 609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.109 Fit side-chains REVERT: A 88 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8132 (t0) REVERT: A 250 VAL cc_start: 0.6235 (OUTLIER) cc_final: 0.5897 (p) REVERT: A 254 MET cc_start: 0.7947 (ttp) cc_final: 0.7694 (mtp) REVERT: A 303 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7226 (mtp85) REVERT: A 430 LYS cc_start: 0.8296 (ttpt) cc_final: 0.7123 (tptt) REVERT: A 456 ARG cc_start: 0.6909 (ttt180) cc_final: 0.5802 (tpm170) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.0865 time to fit residues: 4.0394 Evaluate side-chains 39 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3151 r_free = 0.3151 target = 0.110040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.090192 restraints weight = 3993.001| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.65 r_work: 0.2767 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3479 Z= 0.147 Angle : 0.512 5.433 4761 Z= 0.262 Chirality : 0.038 0.115 551 Planarity : 0.003 0.029 564 Dihedral : 5.081 21.483 588 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.70 % Allowed : 11.90 % Favored : 86.40 % 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: 0.67 (0.43), residues: 405 helix: 0.97 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.61 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 333 TYR 0.012 0.001 TYR A 35 PHE 0.008 0.001 PHE A 372 TRP 0.016 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 3479) covalent geometry : angle 0.51151 / 0.26 ( 4761) hydrogen bonds : bond 0.03563 / 2.34 ( 204) hydrogen bonds : angle 3.92863 / 2.75 ( 609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.065 Fit side-chains REVERT: A 88 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7933 (t0) REVERT: A 207 LYS cc_start: 0.9038 (mmtp) cc_final: 0.8719 (mmtt) REVERT: A 303 ARG cc_start: 0.7806 (ttt-90) cc_final: 0.7184 (mtp85) REVERT: A 429 ARG cc_start: 0.8447 (tpp-160) cc_final: 0.7908 (mmt-90) REVERT: A 430 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7110 (tptt) REVERT: A 456 ARG cc_start: 0.6911 (ttt180) cc_final: 0.5779 (tpm170) outliers start: 6 outliers final: 2 residues processed: 42 average time/residue: 0.0933 time to fit residues: 4.4928 Evaluate side-chains 38 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.110969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.090785 restraints weight = 4011.649| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.65 r_work: 0.2789 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3479 Z= 0.159 Angle : 0.529 5.436 4761 Z= 0.269 Chirality : 0.039 0.117 551 Planarity : 0.003 0.029 564 Dihedral : 5.142 21.791 588 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.13 % Allowed : 12.46 % Favored : 86.40 % 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: 0.68 (0.43), residues: 405 helix: 0.97 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.60 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.015 0.001 TYR A 35 PHE 0.008 0.001 PHE A 372 TRP 0.017 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 3479) covalent geometry : angle 0.52874 / 0.27 ( 4761) hydrogen bonds : bond 0.03643 / 2.39 ( 204) hydrogen bonds : angle 3.97872 / 2.78 ( 609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.146 Fit side-chains REVERT: A 88 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7878 (t0) REVERT: A 207 LYS cc_start: 0.8995 (mmtp) cc_final: 0.8674 (mmtt) REVERT: A 254 MET cc_start: 0.7860 (ttp) cc_final: 0.7632 (mtp) REVERT: A 303 ARG cc_start: 0.7878 (ttt-90) cc_final: 0.7238 (mtp85) REVERT: A 430 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7120 (tptt) REVERT: A 456 ARG cc_start: 0.6950 (ttt180) cc_final: 0.5809 (tpm170) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1156 time to fit residues: 5.0614 Evaluate side-chains 38 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.3980 chunk 39 optimal weight: 0.4980 chunk 3 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.113598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.093375 restraints weight = 3983.357| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.65 r_work: 0.2827 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3479 Z= 0.119 Angle : 0.497 5.356 4761 Z= 0.254 Chirality : 0.037 0.107 551 Planarity : 0.003 0.029 564 Dihedral : 4.992 22.528 588 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.13 % Allowed : 12.46 % Favored : 86.40 % 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: 0.91 (0.43), residues: 405 helix: 1.17 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.62 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 333 TYR 0.012 0.001 TYR A 35 PHE 0.008 0.001 PHE A 372 TRP 0.015 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 3479) covalent geometry : angle 0.49727 / 0.25 ( 4761) hydrogen bonds : bond 0.03443 / 2.25 ( 204) hydrogen bonds : angle 3.87177 / 2.70 ( 609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 798.15 seconds wall clock time: 14 minutes 22.73 seconds (862.73 seconds total)