Starting phenix.real_space_refine on Wed Jul 1 22:58:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kl5_62400/07_2026/9kl5_62400.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kl5_62400/07_2026/9kl5_62400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kl5_62400/07_2026/9kl5_62400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kl5_62400/07_2026/9kl5_62400.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kl5_62400/07_2026/9kl5_62400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kl5_62400/07_2026/9kl5_62400.map" } resolution = 3.33 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= 0.015 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 S 31 5.16 5 Cl 1 4.86 5 C 2395 2.51 5 N 622 2.21 5 O 634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 3683 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3663 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 24, 'TRANS': 449} Chain breaks: 3 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'RTO': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 0.87, per 1000 atoms: 0.24 Number of scatterers: 3683 At special positions: 0 Unit cell: (96.39, 60.75, 71.28, 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) Cl 1 17.00 S 31 16.00 O 634 8.00 N 622 7.00 C 2395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.02 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: 0.21 Conformation dependent library (CDL) restraints added in 87.2 milliseconds 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 80.6% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.631A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 30 Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 130 through 160 removed outlier: 4.051A pdb=" N ARG A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 180 removed outlier: 3.922A pdb=" N VAL A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 212 removed outlier: 3.771A pdb=" N SER A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.514A pdb=" N THR A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 264 removed outlier: 4.175A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.731A pdb=" N PHE A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.553A pdb=" N LYS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 326 through 332 removed outlier: 3.613A pdb=" N LEU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.523A pdb=" N HIS A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 removed outlier: 4.164A pdb=" N VAL A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 392 removed outlier: 3.562A pdb=" N ASN A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 removed outlier: 3.633A pdb=" N ALA A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 449 removed outlier: 3.577A pdb=" N ASN A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 477 removed outlier: 3.568A pdb=" N MET A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 499 removed outlier: 3.570A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.667A pdb=" N LEU A 504 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 236 hydrogen bonds defined for protein. 699 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: 0.37 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1159 1.34 - 1.46: 912 1.46 - 1.58: 1648 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 3768 Sorted by residual: bond pdb=" N04 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.625 1.712 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" N LYS A 382 " pdb=" CA LYS A 382 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" C11 RTO A 601 " pdb=" S08 RTO A 601 " ideal model delta sigma weight residual 1.776 1.820 -0.044 2.00e-02 2.50e+03 4.83e+00 bond pdb=" N ARG A 466 " pdb=" CA ARG A 466 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.28e-02 6.10e+03 4.66e+00 bond pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.54e-01 ... (remaining 3763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 5103 3.62 - 7.23: 22 7.23 - 10.85: 0 10.85 - 14.46: 0 14.46 - 18.08: 1 Bond angle restraints: 5126 Sorted by residual: angle pdb=" O09 RTO A 601 " pdb=" S08 RTO A 601 " pdb=" O10 RTO A 601 " ideal model delta sigma weight residual 119.19 101.11 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C LEU A 126 " pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 122.97 119.86 3.11 9.80e-01 1.04e+00 1.01e+01 angle pdb=" CA LYS A 382 " pdb=" C LYS A 382 " pdb=" O LYS A 382 " ideal model delta sigma weight residual 120.42 117.99 2.43 1.06e+00 8.90e-01 5.28e+00 angle pdb=" N ARG A 466 " pdb=" CA ARG A 466 " pdb=" C ARG A 466 " ideal model delta sigma weight residual 111.82 109.20 2.62 1.16e+00 7.43e-01 5.08e+00 angle pdb=" O18 RTO A 601 " pdb=" C17 RTO A 601 " pdb=" O19 RTO A 601 " ideal model delta sigma weight residual 126.54 120.07 6.47 3.00e+00 1.11e-01 4.65e+00 ... (remaining 5121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 1953 17.90 - 35.81: 205 35.81 - 53.71: 63 53.71 - 71.61: 13 71.61 - 89.51: 3 Dihedral angle restraints: 2237 sinusoidal: 875 harmonic: 1362 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -165.51 79.51 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CB GLU A 270 " pdb=" CG GLU A 270 " pdb=" CD GLU A 270 " pdb=" OE1 GLU A 270 " ideal model delta sinusoidal sigma weight residual 0.00 85.11 -85.11 1 3.00e+01 1.11e-03 9.76e+00 dihedral pdb=" CA GLN A 8 " pdb=" CB GLN A 8 " pdb=" CG GLN A 8 " pdb=" CD GLN A 8 " ideal model delta sinusoidal sigma weight residual -60.00 -118.99 58.99 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 364 0.032 - 0.063: 178 0.063 - 0.095: 32 0.095 - 0.126: 21 0.126 - 0.158: 2 Chirality restraints: 597 Sorted by residual: chirality pdb=" CG LEU A 345 " pdb=" CB LEU A 345 " pdb=" CD1 LEU A 345 " pdb=" CD2 LEU A 345 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE A 110 " pdb=" N ILE A 110 " pdb=" C ILE A 110 " pdb=" CB ILE A 110 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 594 not shown) Planarity restraints: 638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 453 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C ILE A 453 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE A 453 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG A 454 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 418 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" CG ASP A 418 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP A 418 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 418 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 444 " 0.009 2.00e-02 2.50e+03 8.34e-03 1.39e+00 pdb=" CG TYR A 444 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 444 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 444 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 444 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 444 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 444 " 0.001 2.00e-02 2.50e+03 ... (remaining 635 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1297 2.85 - 3.36: 3592 3.36 - 3.87: 6026 3.87 - 4.39: 6903 4.39 - 4.90: 11912 Nonbonded interactions: 29730 Sorted by model distance: nonbonded pdb=" O GLN A 314 " pdb=" OG1 THR A 318 " model vdw 2.337 3.040 nonbonded pdb=" NH1 ARG A 80 " pdb=" OD1 ASP A 107 " model vdw 2.343 3.120 nonbonded pdb=" O SER A 472 " pdb=" OH TYR A 490 " model vdw 2.353 3.040 nonbonded pdb=" OG SER A 231 " pdb=" OD2 ASP A 378 " model vdw 2.372 3.040 nonbonded pdb=" O CYS A 206 " pdb=" ND2 ASN A 210 " model vdw 2.372 3.120 ... (remaining 29725 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.770 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.004 0.087 3770 Z= 0.196 Angle : 0.625 18.079 5130 Z= 0.289 Chirality : 0.039 0.158 597 Planarity : 0.004 0.026 638 Dihedral : 16.280 89.515 1355 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 21.83 % Favored : 78.17 % 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: 0.07 (0.40), residues: 466 helix: 0.16 (0.28), residues: 348 sheet: 0.22 (2.06), residues: 10 loop : 0.16 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.020 0.002 TYR A 444 PHE 0.008 0.001 PHE A 235 TRP 0.009 0.001 TRP A 66 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 3768) covalent geometry : angle 0.62329 / 0.29 ( 5126) SS BOND : bond 0.00785 / 0.38 ( 2) SS BOND : angle 1.87409 / 0.91 ( 4) hydrogen bonds : bond 0.25276 / 16.84 ( 236) hydrogen bonds : angle 7.94720 / 5.69 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0674 time to fit residues: 4.4794 Evaluate side-chains 53 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.099057 restraints weight = 4912.968| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.34 r_work: 0.2994 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3770 Z= 0.154 Angle : 0.561 6.690 5130 Z= 0.282 Chirality : 0.039 0.125 597 Planarity : 0.004 0.025 638 Dihedral : 6.807 58.728 535 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.54 % Allowed : 19.80 % Favored : 77.66 % 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: 1.28 (0.41), residues: 466 helix: 1.09 (0.28), residues: 362 sheet: 0.06 (1.93), residues: 10 loop : 0.37 (0.74), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.015 0.001 TYR A 444 PHE 0.010 0.001 PHE A 258 TRP 0.012 0.002 TRP A 346 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 3768) covalent geometry : angle 0.55995 / 0.28 ( 5126) SS BOND : bond 0.00698 / 0.34 ( 2) SS BOND : angle 1.15165 / 0.66 ( 4) hydrogen bonds : bond 0.05335 / 3.60 ( 236) hydrogen bonds : angle 4.82933 / 3.44 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.124 Fit side-chains REVERT: A 31 MET cc_start: 0.8680 (tpt) cc_final: 0.8474 (mmm) REVERT: A 202 ILE cc_start: 0.7638 (tt) cc_final: 0.7379 (mt) REVERT: A 270 GLU cc_start: 0.8051 (tp30) cc_final: 0.7833 (tp30) REVERT: A 293 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8237 (mtp85) REVERT: A 344 MET cc_start: 0.8334 (tpt) cc_final: 0.8064 (tpp) REVERT: A 503 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8250 (mm) outliers start: 10 outliers final: 5 residues processed: 63 average time/residue: 0.0379 time to fit residues: 3.2035 Evaluate side-chains 56 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 503 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 36 optimal weight: 0.3980 chunk 5 optimal weight: 0.0670 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 0.0470 chunk 2 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 HIS A 168 ASN A 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.103986 restraints weight = 4752.641| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.30 r_work: 0.3055 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3770 Z= 0.103 Angle : 0.486 5.972 5130 Z= 0.237 Chirality : 0.037 0.127 597 Planarity : 0.003 0.024 638 Dihedral : 6.282 54.572 535 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.28 % Allowed : 21.32 % Favored : 76.40 % 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: 1.91 (0.42), residues: 466 helix: 1.54 (0.29), residues: 361 sheet: 0.73 (2.12), residues: 10 loop : 0.54 (0.76), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.010 0.001 TYR A 444 PHE 0.006 0.001 PHE A 339 TRP 0.009 0.001 TRP A 274 HIS 0.001 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 3768) covalent geometry : angle 0.48568 / 0.24 ( 5126) SS BOND : bond 0.00393 / 0.19 ( 2) SS BOND : angle 0.91307 / 0.52 ( 4) hydrogen bonds : bond 0.03975 / 2.64 ( 236) hydrogen bonds : angle 4.23555 / 3.00 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.128 Fit side-chains REVERT: A 5 ASP cc_start: 0.8946 (m-30) cc_final: 0.8718 (t0) REVERT: A 66 TRP cc_start: 0.7102 (m100) cc_final: 0.6809 (m100) REVERT: A 293 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8155 (mtp85) REVERT: A 344 MET cc_start: 0.8266 (tpt) cc_final: 0.8055 (tpp) REVERT: A 503 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8268 (mm) outliers start: 9 outliers final: 2 residues processed: 58 average time/residue: 0.0471 time to fit residues: 3.4884 Evaluate side-chains 55 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 503 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.129072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102218 restraints weight = 4822.556| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.31 r_work: 0.3034 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3770 Z= 0.136 Angle : 0.496 5.223 5130 Z= 0.245 Chirality : 0.038 0.129 597 Planarity : 0.003 0.025 638 Dihedral : 6.254 53.806 535 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.55 % Allowed : 19.80 % Favored : 76.65 % 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: 1.99 (0.42), residues: 466 helix: 1.60 (0.29), residues: 361 sheet: 0.61 (2.02), residues: 10 loop : 0.57 (0.75), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.012 0.001 TYR A 264 PHE 0.008 0.001 PHE A 235 TRP 0.009 0.001 TRP A 247 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 3768) covalent geometry : angle 0.49536 / 0.24 ( 5126) SS BOND : bond 0.00623 / 0.30 ( 2) SS BOND : angle 1.06933 / 0.57 ( 4) hydrogen bonds : bond 0.03994 / 2.66 ( 236) hydrogen bonds : angle 4.16500 / 2.95 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.084 Fit side-chains REVERT: A 5 ASP cc_start: 0.8955 (m-30) cc_final: 0.8728 (t0) REVERT: A 66 TRP cc_start: 0.7064 (m100) cc_final: 0.6821 (m100) REVERT: A 112 ASP cc_start: 0.8350 (t0) cc_final: 0.8060 (t0) outliers start: 14 outliers final: 8 residues processed: 65 average time/residue: 0.0354 time to fit residues: 3.1490 Evaluate side-chains 62 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 0.0570 chunk 26 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102960 restraints weight = 4767.264| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.29 r_work: 0.3041 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3770 Z= 0.133 Angle : 0.515 6.348 5130 Z= 0.252 Chirality : 0.039 0.157 597 Planarity : 0.003 0.026 638 Dihedral : 6.233 52.686 535 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.79 % Allowed : 20.30 % Favored : 76.90 % 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: 2.10 (0.42), residues: 466 helix: 1.62 (0.29), residues: 362 sheet: 0.44 (1.90), residues: 10 loop : 0.91 (0.78), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.012 0.001 TYR A 264 PHE 0.008 0.001 PHE A 235 TRP 0.008 0.001 TRP A 247 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 3768) covalent geometry : angle 0.51147 / 0.25 ( 5126) SS BOND : bond 0.00256 / 0.13 ( 2) SS BOND : angle 2.14773 / 1.17 ( 4) hydrogen bonds : bond 0.03828 / 2.55 ( 236) hydrogen bonds : angle 4.08575 / 2.89 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.130 Fit side-chains REVERT: A 5 ASP cc_start: 0.8924 (m-30) cc_final: 0.8723 (t0) REVERT: A 31 MET cc_start: 0.8658 (mmm) cc_final: 0.8368 (mmm) REVERT: A 66 TRP cc_start: 0.7109 (m100) cc_final: 0.6906 (m100) REVERT: A 112 ASP cc_start: 0.8362 (t0) cc_final: 0.8066 (t0) REVERT: A 293 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8202 (mtp85) outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.0452 time to fit residues: 3.7391 Evaluate side-chains 60 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.103750 restraints weight = 4783.946| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.30 r_work: 0.3048 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3770 Z= 0.128 Angle : 0.498 5.643 5130 Z= 0.244 Chirality : 0.038 0.132 597 Planarity : 0.003 0.026 638 Dihedral : 6.188 51.846 535 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.05 % Allowed : 20.56 % Favored : 76.40 % 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: 2.15 (0.42), residues: 466 helix: 1.66 (0.29), residues: 363 sheet: 0.30 (1.85), residues: 10 loop : 0.94 (0.79), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.011 0.001 TYR A 264 PHE 0.007 0.001 PHE A 235 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 3768) covalent geometry : angle 0.49440 / 0.24 ( 5126) SS BOND : bond 0.00689 / 0.33 ( 2) SS BOND : angle 2.19355 / 1.13 ( 4) hydrogen bonds : bond 0.03727 / 2.48 ( 236) hydrogen bonds : angle 4.02831 / 2.85 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.083 Fit side-chains REVERT: A 31 MET cc_start: 0.8677 (mmm) cc_final: 0.8384 (mmm) REVERT: A 112 ASP cc_start: 0.8295 (t0) cc_final: 0.7978 (t0) REVERT: A 293 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8208 (mtp85) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.0443 time to fit residues: 3.7462 Evaluate side-chains 62 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.103208 restraints weight = 4916.167| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.34 r_work: 0.3043 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3770 Z= 0.131 Angle : 0.510 5.780 5130 Z= 0.253 Chirality : 0.038 0.131 597 Planarity : 0.003 0.026 638 Dihedral : 6.182 51.631 535 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.79 % Allowed : 20.56 % Favored : 76.65 % 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: 2.19 (0.42), residues: 466 helix: 1.68 (0.29), residues: 363 sheet: 0.36 (1.85), residues: 10 loop : 0.95 (0.79), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.011 0.001 TYR A 264 PHE 0.022 0.001 PHE A 351 TRP 0.011 0.001 TRP A 66 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 3768) covalent geometry : angle 0.50802 / 0.25 ( 5126) SS BOND : bond 0.00702 / 0.34 ( 2) SS BOND : angle 1.78607 / 0.88 ( 4) hydrogen bonds : bond 0.03723 / 2.48 ( 236) hydrogen bonds : angle 4.02291 / 2.85 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.083 Fit side-chains REVERT: A 31 MET cc_start: 0.8659 (mmm) cc_final: 0.8355 (mmm) REVERT: A 112 ASP cc_start: 0.8290 (t0) cc_final: 0.7977 (t0) REVERT: A 293 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8196 (mtp85) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.0482 time to fit residues: 3.9688 Evaluate side-chains 61 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.130326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103089 restraints weight = 4852.372| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.32 r_work: 0.3049 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3770 Z= 0.127 Angle : 0.509 5.986 5130 Z= 0.251 Chirality : 0.038 0.131 597 Planarity : 0.003 0.026 638 Dihedral : 6.179 51.917 535 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.79 % Allowed : 20.56 % Favored : 76.65 % 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: 2.21 (0.42), residues: 466 helix: 1.70 (0.29), residues: 363 sheet: 0.52 (1.89), residues: 10 loop : 0.90 (0.79), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.011 0.001 TYR A 264 PHE 0.018 0.001 PHE A 351 TRP 0.010 0.001 TRP A 66 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 3768) covalent geometry : angle 0.50639 / 0.25 ( 5126) SS BOND : bond 0.00722 / 0.35 ( 2) SS BOND : angle 1.78323 / 0.90 ( 4) hydrogen bonds : bond 0.03675 / 2.45 ( 236) hydrogen bonds : angle 4.00554 / 2.84 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.150 Fit side-chains REVERT: A 31 MET cc_start: 0.8677 (mmm) cc_final: 0.8380 (mmm) REVERT: A 112 ASP cc_start: 0.8311 (t0) cc_final: 0.7987 (t0) REVERT: A 293 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8189 (mtp85) outliers start: 11 outliers final: 8 residues processed: 62 average time/residue: 0.0485 time to fit residues: 3.9192 Evaluate side-chains 61 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.0370 chunk 39 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102625 restraints weight = 4849.233| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.30 r_work: 0.3035 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3770 Z= 0.133 Angle : 0.515 6.019 5130 Z= 0.255 Chirality : 0.039 0.131 597 Planarity : 0.003 0.026 638 Dihedral : 6.183 52.048 535 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.79 % Allowed : 20.56 % Favored : 76.65 % 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: 2.25 (0.42), residues: 466 helix: 1.73 (0.29), residues: 362 sheet: 0.59 (1.91), residues: 10 loop : 0.94 (0.77), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.012 0.001 TYR A 264 PHE 0.016 0.001 PHE A 351 TRP 0.010 0.001 TRP A 66 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 3768) covalent geometry : angle 0.51281 / 0.25 ( 5126) SS BOND : bond 0.00735 / 0.35 ( 2) SS BOND : angle 1.63251 / 0.85 ( 4) hydrogen bonds : bond 0.03727 / 2.48 ( 236) hydrogen bonds : angle 4.00564 / 2.84 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.084 Fit side-chains REVERT: A 112 ASP cc_start: 0.8317 (t0) cc_final: 0.8000 (t0) REVERT: A 293 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8217 (mtp85) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.0431 time to fit residues: 3.5795 Evaluate side-chains 61 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101911 restraints weight = 4885.166| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.32 r_work: 0.3029 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3770 Z= 0.150 Angle : 0.538 6.000 5130 Z= 0.265 Chirality : 0.040 0.132 597 Planarity : 0.004 0.026 638 Dihedral : 6.233 52.152 535 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.05 % Allowed : 20.30 % Favored : 76.65 % 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: 2.23 (0.42), residues: 466 helix: 1.70 (0.29), residues: 361 sheet: 0.44 (1.86), residues: 10 loop : 1.01 (0.77), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.012 0.001 TYR A 264 PHE 0.014 0.001 PHE A 351 TRP 0.010 0.001 TRP A 66 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 3768) covalent geometry : angle 0.53563 / 0.26 ( 5126) SS BOND : bond 0.00798 / 0.38 ( 2) SS BOND : angle 1.89769 / 0.97 ( 4) hydrogen bonds : bond 0.03867 / 2.58 ( 236) hydrogen bonds : angle 4.04480 / 2.87 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.125 Fit side-chains REVERT: A 112 ASP cc_start: 0.8332 (t0) cc_final: 0.8019 (t0) REVERT: A 293 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8233 (mtp85) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.0572 time to fit residues: 4.7953 Evaluate side-chains 60 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 45 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.104420 restraints weight = 4737.773| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.28 r_work: 0.3058 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3770 Z= 0.114 Angle : 0.516 6.391 5130 Z= 0.253 Chirality : 0.038 0.131 597 Planarity : 0.003 0.026 638 Dihedral : 6.182 53.499 535 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.03 % Allowed : 21.07 % Favored : 76.90 % 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: 2.32 (0.42), residues: 466 helix: 1.79 (0.29), residues: 361 sheet: 0.21 (1.78), residues: 10 loop : 0.96 (0.76), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.010 0.001 TYR A 264 PHE 0.014 0.001 PHE A 351 TRP 0.012 0.001 TRP A 66 HIS 0.002 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 3768) covalent geometry : angle 0.51497 / 0.25 ( 5126) SS BOND : bond 0.00650 / 0.31 ( 2) SS BOND : angle 1.45862 / 0.75 ( 4) hydrogen bonds : bond 0.03553 / 2.35 ( 236) hydrogen bonds : angle 3.97289 / 2.81 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 960.89 seconds wall clock time: 17 minutes 7.49 seconds (1027.49 seconds total)