Starting phenix.real_space_refine on Tue Mar 3 13:51:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugx_26498/03_2026/7ugx_26498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugx_26498/03_2026/7ugx_26498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ugx_26498/03_2026/7ugx_26498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugx_26498/03_2026/7ugx_26498.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ugx_26498/03_2026/7ugx_26498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugx_26498/03_2026/7ugx_26498.map" } resolution = 2.96 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= 0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2999 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians S 16 5.16 5 Na 3 4.78 5 C 2041 2.51 5 N 505 2.21 5 O 542 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3108 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3093 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 416, 3093 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3140 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 10 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 10 " occ=0.50 Time building chain proxies: 1.22, per 1000 atoms: 0.39 Number of scatterers: 3108 At special positions: 0 Unit cell: (77.532, 74.976, 71.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 Na 3 11.00 F 1 9.00 O 542 8.00 N 505 7.00 C 2041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 206.8 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.649A pdb=" N ILE A 8 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 33 Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.707A pdb=" N VAL A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.550A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.540A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 107 removed outlier: 3.578A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.954A pdb=" N GLN A 120 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.734A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 170 removed outlier: 3.775A pdb=" N THR A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 220 removed outlier: 3.529A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 222 through 246 removed outlier: 3.941A pdb=" N GLY A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.511A pdb=" N TYR A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.583A pdb=" N LYS A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.544A pdb=" N TYR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 4.515A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.542A pdb=" N ALA A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.792A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.740A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.783A pdb=" N GLY A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE A 389 " --> pdb=" O EFC A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 415 removed outlier: 3.652A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) 228 hydrogen bonds defined for protein. 681 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: 0.48 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 984 1.37 - 1.55: 2153 1.55 - 1.74: 0 1.74 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3168 Sorted by residual: bond pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 2.054 2.101 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C EFC A 385 " pdb=" O EFC A 385 " ideal model delta sigma weight residual 1.231 1.186 0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" N MET A 311 " pdb=" CA MET A 311 " ideal model delta sigma weight residual 1.463 1.489 -0.026 1.31e-02 5.83e+03 3.92e+00 bond pdb=" C2 EFC A 385 " pdb=" F2 EFC A 385 " ideal model delta sigma weight residual 1.388 1.365 0.023 2.00e-02 2.50e+03 1.36e+00 bond pdb=" C1 EFC A 385 " pdb=" C2 EFC A 385 " ideal model delta sigma weight residual 1.506 1.528 -0.022 2.00e-02 2.50e+03 1.18e+00 ... (remaining 3163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4247 1.56 - 3.13: 56 3.13 - 4.69: 14 4.69 - 6.26: 4 6.26 - 7.82: 1 Bond angle restraints: 4322 Sorted by residual: angle pdb=" CA MET A 311 " pdb=" C MET A 311 " pdb=" O MET A 311 " ideal model delta sigma weight residual 122.37 118.54 3.83 1.15e+00 7.56e-01 1.11e+01 angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 109.47 -7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" N MET A 59 " pdb=" CA MET A 59 " pdb=" C MET A 59 " ideal model delta sigma weight residual 109.81 114.19 -4.38 2.21e+00 2.05e-01 3.93e+00 angle pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " pdb=" C1 EFC A 385 " ideal model delta sigma weight residual 103.98 109.75 -5.77 3.00e+00 1.11e-01 3.71e+00 angle pdb=" N ILE A 389 " pdb=" CA ILE A 389 " pdb=" C ILE A 389 " ideal model delta sigma weight residual 109.34 113.31 -3.97 2.08e+00 2.31e-01 3.65e+00 ... (remaining 4317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.09: 1717 15.09 - 30.19: 110 30.19 - 45.28: 23 45.28 - 60.38: 3 60.38 - 75.47: 2 Dihedral angle restraints: 1855 sinusoidal: 671 harmonic: 1184 Sorted by residual: dihedral pdb=" CG ARG A 105 " pdb=" CD ARG A 105 " pdb=" NE ARG A 105 " pdb=" CZ ARG A 105 " ideal model delta sinusoidal sigma weight residual 90.00 130.21 -40.21 2 1.50e+01 4.44e-03 8.89e+00 dihedral pdb=" CB MET A 103 " pdb=" CG MET A 103 " pdb=" SD MET A 103 " pdb=" CE MET A 103 " ideal model delta sinusoidal sigma weight residual 60.00 102.30 -42.30 3 1.50e+01 4.44e-03 7.59e+00 dihedral pdb=" CB MET A 292 " pdb=" CG MET A 292 " pdb=" SD MET A 292 " pdb=" CE MET A 292 " ideal model delta sinusoidal sigma weight residual 60.00 102.23 -42.23 3 1.50e+01 4.44e-03 7.57e+00 ... (remaining 1852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 306 0.023 - 0.046: 118 0.046 - 0.069: 87 0.069 - 0.091: 19 0.091 - 0.114: 9 Chirality restraints: 539 Sorted by residual: chirality pdb=" CA MET A 59 " pdb=" N MET A 59 " pdb=" C MET A 59 " pdb=" CB MET A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" C PRO A 258 " pdb=" CB PRO A 258 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.91e-01 chirality pdb=" CA ILE A 294 " pdb=" N ILE A 294 " pdb=" C ILE A 294 " pdb=" CB ILE A 294 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 536 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 45 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 394 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" CG ASP A 394 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP A 394 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 394 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 108 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 109 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " -0.019 5.00e-02 4.00e+02 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 570 2.77 - 3.30: 3221 3.30 - 3.83: 4843 3.83 - 4.37: 5536 4.37 - 4.90: 9605 Nonbonded interactions: 23775 Sorted by model distance: nonbonded pdb=" O SER A 349 " pdb="NA NA A 503 " model vdw 2.234 2.470 nonbonded pdb=" OG SER A 278 " pdb=" OXT ASP A 501 " model vdw 2.413 3.040 nonbonded pdb=" O THR A 308 " pdb="NA NA A 503 " model vdw 2.425 2.470 nonbonded pdb=" OG1 THR A 398 " pdb=" N ASP A 501 " model vdw 2.425 3.120 nonbonded pdb=" O GLY A 221 " pdb=" N HIS A 223 " model vdw 2.426 3.120 ... (remaining 23770 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=0.50 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.830 Find NCS groups from input model: 0.010 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.002 0.047 3168 Z= 0.114 Angle : 0.495 7.822 4322 Z= 0.243 Chirality : 0.035 0.114 539 Planarity : 0.004 0.044 534 Dihedral : 10.608 75.469 1105 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.39), residues: 413 helix: 1.49 (0.27), residues: 324 sheet: None (None), residues: 0 loop : 0.40 (0.69), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.010 0.001 TYR A 299 PHE 0.005 0.001 PHE A 210 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 3168) covalent geometry : angle 0.49528 ( 4322) hydrogen bonds : bond 0.28026 ( 228) hydrogen bonds : angle 5.83297 ( 681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.111 Fit side-chains REVERT: A 202 MET cc_start: 0.8380 (mmt) cc_final: 0.8111 (mmt) REVERT: A 245 LEU cc_start: 0.9124 (tp) cc_final: 0.8884 (tt) REVERT: A 257 ASP cc_start: 0.8731 (t0) cc_final: 0.8430 (t0) REVERT: A 267 ASP cc_start: 0.8865 (m-30) cc_final: 0.8637 (m-30) REVERT: A 269 MET cc_start: 0.8906 (mtp) cc_final: 0.8645 (mtm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.4499 time to fit residues: 30.1890 Evaluate side-chains 46 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.116552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076490 restraints weight = 6080.095| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.49 r_work: 0.2960 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3168 Z= 0.173 Angle : 0.651 8.156 4322 Z= 0.330 Chirality : 0.041 0.166 539 Planarity : 0.005 0.046 534 Dihedral : 3.811 27.260 446 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.85 % Allowed : 12.04 % Favored : 86.11 % 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: 2.65 (0.41), residues: 413 helix: 2.18 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 0.23 (0.68), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 287 TYR 0.021 0.002 TYR A 317 PHE 0.014 0.002 PHE A 261 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3168) covalent geometry : angle 0.65089 ( 4322) hydrogen bonds : bond 0.06715 ( 228) hydrogen bonds : angle 4.12016 ( 681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.112 Fit side-chains REVERT: A 245 LEU cc_start: 0.8959 (tp) cc_final: 0.8741 (tt) REVERT: A 399 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7913 (tpp) REVERT: A 405 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7358 (m-30) outliers start: 6 outliers final: 1 residues processed: 51 average time/residue: 0.5061 time to fit residues: 26.6460 Evaluate side-chains 49 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.116730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.076774 restraints weight = 6037.512| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.52 r_work: 0.2936 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3168 Z= 0.135 Angle : 0.576 6.757 4322 Z= 0.286 Chirality : 0.039 0.155 539 Planarity : 0.005 0.049 534 Dihedral : 3.701 23.802 446 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.93 % Allowed : 15.74 % Favored : 83.33 % 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: 2.88 (0.41), residues: 413 helix: 2.32 (0.28), residues: 328 sheet: None (None), residues: 0 loop : 0.31 (0.70), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 287 TYR 0.018 0.001 TYR A 317 PHE 0.012 0.001 PHE A 261 HIS 0.002 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3168) covalent geometry : angle 0.57626 ( 4322) hydrogen bonds : bond 0.05328 ( 228) hydrogen bonds : angle 3.79481 ( 681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.117 Fit side-chains REVERT: A 405 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7044 (m-30) outliers start: 3 outliers final: 0 residues processed: 48 average time/residue: 0.4498 time to fit residues: 22.3012 Evaluate side-chains 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.0060 chunk 36 optimal weight: 0.1980 chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.118736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.079097 restraints weight = 6043.627| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.52 r_work: 0.2981 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3168 Z= 0.120 Angle : 0.576 9.329 4322 Z= 0.280 Chirality : 0.038 0.147 539 Planarity : 0.005 0.051 534 Dihedral : 3.583 23.909 446 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.93 % Allowed : 16.36 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.42), residues: 413 helix: 2.40 (0.28), residues: 328 sheet: None (None), residues: 0 loop : 0.47 (0.73), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 287 TYR 0.015 0.001 TYR A 317 PHE 0.010 0.001 PHE A 261 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3168) covalent geometry : angle 0.57590 ( 4322) hydrogen bonds : bond 0.04466 ( 228) hydrogen bonds : angle 3.58732 ( 681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.110 Fit side-chains REVERT: A 405 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.6956 (m-30) outliers start: 3 outliers final: 0 residues processed: 48 average time/residue: 0.4215 time to fit residues: 20.9935 Evaluate side-chains 46 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.115200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.074672 restraints weight = 6009.243| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.51 r_work: 0.2906 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3168 Z= 0.154 Angle : 0.615 8.195 4322 Z= 0.296 Chirality : 0.040 0.137 539 Planarity : 0.005 0.050 534 Dihedral : 3.641 24.520 446 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.85 % Allowed : 17.28 % Favored : 80.86 % 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: 2.91 (0.42), residues: 413 helix: 2.29 (0.28), residues: 329 sheet: None (None), residues: 0 loop : 0.54 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.015 0.001 TYR A 299 PHE 0.010 0.001 PHE A 261 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3168) covalent geometry : angle 0.61455 ( 4322) hydrogen bonds : bond 0.05534 ( 228) hydrogen bonds : angle 3.74888 ( 681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.120 Fit side-chains REVERT: A 227 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8483 (mp0) REVERT: A 399 MET cc_start: 0.8188 (mmm) cc_final: 0.7867 (tpt) REVERT: A 405 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7417 (t0) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.4544 time to fit residues: 23.0291 Evaluate side-chains 47 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.117743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077554 restraints weight = 6014.369| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.53 r_work: 0.2948 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3168 Z= 0.121 Angle : 0.579 11.024 4322 Z= 0.279 Chirality : 0.039 0.171 539 Planarity : 0.005 0.051 534 Dihedral : 3.556 19.244 446 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.54 % Allowed : 18.52 % Favored : 79.94 % 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: 2.99 (0.42), residues: 413 helix: 2.32 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.61 (0.78), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.013 0.001 TYR A 317 PHE 0.010 0.001 PHE A 261 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3168) covalent geometry : angle 0.57890 ( 4322) hydrogen bonds : bond 0.04589 ( 228) hydrogen bonds : angle 3.60676 ( 681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.071 Fit side-chains REVERT: A 405 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7379 (t0) outliers start: 5 outliers final: 0 residues processed: 48 average time/residue: 0.4773 time to fit residues: 23.7122 Evaluate side-chains 45 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076617 restraints weight = 6051.103| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.48 r_work: 0.2935 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3168 Z= 0.133 Angle : 0.589 8.069 4322 Z= 0.284 Chirality : 0.039 0.182 539 Planarity : 0.005 0.050 534 Dihedral : 3.536 21.083 446 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.93 % Allowed : 20.37 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.42), residues: 413 helix: 2.28 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.61 (0.78), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.014 0.001 TYR A 299 PHE 0.010 0.001 PHE A 261 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3168) covalent geometry : angle 0.58862 ( 4322) hydrogen bonds : bond 0.04988 ( 228) hydrogen bonds : angle 3.65773 ( 681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.177 Fit side-chains REVERT: A 405 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7378 (t0) outliers start: 3 outliers final: 0 residues processed: 47 average time/residue: 0.4869 time to fit residues: 23.6551 Evaluate side-chains 44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.118132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078002 restraints weight = 6100.373| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.56 r_work: 0.2950 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3168 Z= 0.120 Angle : 0.607 9.647 4322 Z= 0.285 Chirality : 0.039 0.200 539 Planarity : 0.005 0.050 534 Dihedral : 3.497 17.890 446 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.54 % Allowed : 20.99 % Favored : 77.47 % 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: 3.02 (0.42), residues: 413 helix: 2.34 (0.28), residues: 334 sheet: None (None), residues: 0 loop : 0.58 (0.79), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.013 0.001 TYR A 299 PHE 0.009 0.001 PHE A 261 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3168) covalent geometry : angle 0.60653 ( 4322) hydrogen bonds : bond 0.04507 ( 228) hydrogen bonds : angle 3.58038 ( 681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.113 Fit side-chains REVERT: A 267 ASP cc_start: 0.8927 (m-30) cc_final: 0.8691 (m-30) REVERT: A 405 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7308 (t0) outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 0.5060 time to fit residues: 24.5623 Evaluate side-chains 47 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.117360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.077100 restraints weight = 6053.655| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.48 r_work: 0.2938 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3168 Z= 0.132 Angle : 0.617 9.576 4322 Z= 0.294 Chirality : 0.039 0.153 539 Planarity : 0.005 0.050 534 Dihedral : 3.504 19.517 446 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.93 % Allowed : 22.22 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.43), residues: 413 helix: 2.33 (0.29), residues: 333 sheet: None (None), residues: 0 loop : 0.63 (0.79), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 287 TYR 0.014 0.001 TYR A 299 PHE 0.010 0.001 PHE A 261 HIS 0.002 0.000 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3168) covalent geometry : angle 0.61732 ( 4322) hydrogen bonds : bond 0.04787 ( 228) hydrogen bonds : angle 3.59408 ( 681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.116 Fit side-chains REVERT: A 267 ASP cc_start: 0.8927 (m-30) cc_final: 0.8690 (m-30) REVERT: A 405 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7356 (t0) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.4324 time to fit residues: 21.9335 Evaluate side-chains 49 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 405 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.116013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075351 restraints weight = 6036.099| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.52 r_work: 0.2904 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3168 Z= 0.154 Angle : 0.654 14.381 4322 Z= 0.308 Chirality : 0.040 0.204 539 Planarity : 0.005 0.050 534 Dihedral : 3.637 19.985 446 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.93 % Allowed : 22.84 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.43), residues: 413 helix: 2.23 (0.29), residues: 333 sheet: None (None), residues: 0 loop : 0.68 (0.78), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 287 TYR 0.015 0.001 TYR A 299 PHE 0.009 0.001 PHE A 261 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3168) covalent geometry : angle 0.65400 ( 4322) hydrogen bonds : bond 0.05301 ( 228) hydrogen bonds : angle 3.67110 ( 681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.111 Fit side-chains REVERT: A 267 ASP cc_start: 0.8926 (m-30) cc_final: 0.8683 (m-30) REVERT: A 310 ASN cc_start: 0.8575 (t0) cc_final: 0.8305 (t0) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.4954 time to fit residues: 25.0495 Evaluate side-chains 45 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.116978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.076812 restraints weight = 6068.391| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.50 r_work: 0.2930 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3168 Z= 0.137 Angle : 0.651 14.985 4322 Z= 0.312 Chirality : 0.039 0.204 539 Planarity : 0.005 0.050 534 Dihedral : 3.617 19.673 446 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.31 % Allowed : 22.53 % Favored : 77.16 % 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: 2.85 (0.43), residues: 413 helix: 2.21 (0.29), residues: 333 sheet: None (None), residues: 0 loop : 0.60 (0.79), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 287 TYR 0.014 0.001 TYR A 299 PHE 0.009 0.001 PHE A 261 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3168) covalent geometry : angle 0.65085 ( 4322) hydrogen bonds : bond 0.04882 ( 228) hydrogen bonds : angle 3.63644 ( 681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1504.09 seconds wall clock time: 26 minutes 14.02 seconds (1574.02 seconds total)