Starting phenix.real_space_refine on Wed Jul 1 22:50:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9klz_62418/07_2026/9klz_62418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9klz_62418/07_2026/9klz_62418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9klz_62418/07_2026/9klz_62418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9klz_62418/07_2026/9klz_62418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9klz_62418/07_2026/9klz_62418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9klz_62418/07_2026/9klz_62418.map" } resolution = 3.88 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= 0.051 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 28 5.16 5 Cl 1 4.86 5 C 2348 2.51 5 N 606 2.21 5 O 616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3599 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3565 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 26, 'TRANS': 436} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'OLM': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 0.99, per 1000 atoms: 0.28 Number of scatterers: 3599 At special positions: 0 Unit cell: (98.67, 58.344, 71.214, 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 28 16.00 O 616 8.00 N 606 7.00 C 2348 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=2.03 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: 0.30 Conformation dependent library (CDL) restraints added in 85.9 milliseconds 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 856 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 80.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.774A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 removed outlier: 3.526A pdb=" N ILE A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 36 removed outlier: 3.844A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN A 35 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 42 removed outlier: 4.224A pdb=" N PHE A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 130 through 159 removed outlier: 4.447A pdb=" N ARG A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 180 removed outlier: 3.617A pdb=" N VAL A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.518A pdb=" N LEU A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.550A pdb=" N THR A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.503A pdb=" N SER A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.666A pdb=" N ILE A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.728A pdb=" N HIS A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'A' and resid 332 through 358 removed outlier: 4.269A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.531A pdb=" N GLY A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.533A pdb=" N ARG A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 475 removed outlier: 3.523A pdb=" N MET A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 468 " --> pdb=" O MET A 464 " (cutoff:3.500A) Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 484 through 498 removed outlier: 3.525A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 499 through 504 removed outlier: 4.183A pdb=" N VAL A 502 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 removed outlier: 4.274A pdb=" N GLU A 520 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.674A pdb=" N HIS A 48 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 202 hydrogen bonds defined for protein. 585 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: 0.40 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1118 1.34 - 1.46: 640 1.46 - 1.58: 1889 1.58 - 1.70: 1 1.70 - 1.82: 43 Bond restraints: 3691 Sorted by residual: bond pdb=" C15 OLM A 601 " pdb=" C18 OLM A 601 " ideal model delta sigma weight residual 1.491 1.585 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C5 OLM A 601 " pdb=" C8 OLM A 601 " ideal model delta sigma weight residual 1.479 1.563 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N GLU A 480 " pdb=" CA GLU A 480 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.20e-02 6.94e+03 5.62e+00 bond pdb=" N SER A 484 " pdb=" CA SER A 484 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.33e-02 5.65e+03 5.27e+00 bond pdb=" N LEU A 481 " pdb=" CA LEU A 481 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.18e-02 7.18e+03 5.24e+00 ... (remaining 3686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 4957 2.39 - 4.78: 67 4.78 - 7.17: 9 7.17 - 9.56: 1 9.56 - 11.95: 3 Bond angle restraints: 5037 Sorted by residual: angle pdb=" CA LEU A 159 " pdb=" CB LEU A 159 " pdb=" CG LEU A 159 " ideal model delta sigma weight residual 116.30 128.25 -11.95 3.50e+00 8.16e-02 1.17e+01 angle pdb=" CB MET A 214 " pdb=" CG MET A 214 " pdb=" SD MET A 214 " ideal model delta sigma weight residual 112.70 122.41 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CA LEU A 281 " pdb=" CB LEU A 281 " pdb=" CG LEU A 281 " ideal model delta sigma weight residual 116.30 126.12 -9.82 3.50e+00 8.16e-02 7.87e+00 angle pdb=" CA GLU A 480 " pdb=" C GLU A 480 " pdb=" O GLU A 480 " ideal model delta sigma weight residual 120.90 118.11 2.79 1.07e+00 8.73e-01 6.78e+00 angle pdb=" CA LEU A 481 " pdb=" C LEU A 481 " pdb=" O LEU A 481 " ideal model delta sigma weight residual 120.90 118.22 2.68 1.03e+00 9.43e-01 6.76e+00 ... (remaining 5032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.11: 2064 34.11 - 68.23: 89 68.23 - 102.34: 4 102.34 - 136.45: 0 136.45 - 170.56: 1 Dihedral angle restraints: 2158 sinusoidal: 827 harmonic: 1331 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 -151.26 65.26 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual 93.00 151.57 -58.57 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" C3 OLM A 601 " pdb=" C1 OLM A 601 " pdb=" C2 OLM A 601 " pdb=" N1 OLM A 601 " ideal model delta sinusoidal sigma weight residual -125.43 45.13 -170.56 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 2155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 376 0.030 - 0.060: 145 0.060 - 0.090: 42 0.090 - 0.120: 15 0.120 - 0.150: 5 Chirality restraints: 583 Sorted by residual: chirality pdb=" CB ILE A 453 " pdb=" CA ILE A 453 " pdb=" CG1 ILE A 453 " pdb=" CG2 ILE A 453 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CB ILE A 44 " pdb=" CA ILE A 44 " pdb=" CG1 ILE A 44 " pdb=" CG2 ILE A 44 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CG LEU A 283 " pdb=" CB LEU A 283 " pdb=" CD1 LEU A 283 " pdb=" CD2 LEU A 283 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 580 not shown) Planarity restraints: 628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 504 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 505 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 505 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 505 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 44 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 45 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " -0.014 5.00e-02 4.00e+02 2.14e-02 7.36e-01 pdb=" N PRO A 27 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.012 5.00e-02 4.00e+02 ... (remaining 625 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1271 2.85 - 3.37: 3499 3.37 - 3.88: 5527 3.88 - 4.39: 6132 4.39 - 4.90: 10141 Nonbonded interactions: 26570 Sorted by model distance: nonbonded pdb=" O ALA A 42 " pdb=" NH2 ARG A 134 " model vdw 2.344 3.120 nonbonded pdb=" NH1 ARG A 395 " pdb=" O LEU A 504 " model vdw 2.349 3.120 nonbonded pdb=" O THR A 119 " pdb=" OG1 THR A 122 " model vdw 2.362 3.040 nonbonded pdb=" O SER A 472 " pdb=" OH TYR A 490 " model vdw 2.398 3.040 nonbonded pdb=" N ASP A 70 " pdb=" O GLN A 74 " model vdw 2.412 3.120 ... (remaining 26565 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.740 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.094 3693 Z= 0.208 Angle : 0.640 11.951 5041 Z= 0.282 Chirality : 0.038 0.150 583 Planarity : 0.003 0.026 628 Dihedral : 17.438 170.562 1296 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 26.77 % Favored : 73.23 % 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: 0.22 (0.40), residues: 455 helix: 0.55 (0.30), residues: 308 sheet: None (None), residues: 0 loop : -0.51 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.011 0.001 TYR A 490 PHE 0.005 0.000 PHE A 262 TRP 0.012 0.001 TRP A 247 HIS 0.005 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.21 ( 3691) covalent geometry : angle 0.64038 / 0.28 ( 5037) SS BOND : bond 0.00078 / 0.04 ( 2) SS BOND : angle 0.69755 / 0.27 ( 4) hydrogen bonds : bond 0.32548 / 22.16 ( 202) hydrogen bonds : angle 7.06243 / 5.21 ( 585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8502 (tt) cc_final: 0.7918 (mp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0381 time to fit residues: 3.6630 Evaluate side-chains 67 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 HIS A 371 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116901 restraints weight = 6988.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120511 restraints weight = 3678.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122965 restraints weight = 2456.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124192 restraints weight = 1908.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125195 restraints weight = 1661.196| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3693 Z= 0.159 Angle : 0.644 9.718 5041 Z= 0.314 Chirality : 0.040 0.127 583 Planarity : 0.004 0.030 628 Dihedral : 10.823 176.186 514 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.72 % Allowed : 24.67 % Favored : 70.60 % 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: 0.97 (0.41), residues: 455 helix: 1.34 (0.30), residues: 305 sheet: -1.05 (1.51), residues: 10 loop : -0.68 (0.56), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 248 TYR 0.012 0.001 TYR A 490 PHE 0.010 0.001 PHE A 185 TRP 0.013 0.001 TRP A 346 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 ( 3691) covalent geometry : angle 0.64444 / 0.31 ( 5037) SS BOND : bond 0.00042 / 0.02 ( 2) SS BOND : angle 0.33433 / 0.21 ( 4) hydrogen bonds : bond 0.08002 / 5.39 ( 202) hydrogen bonds : angle 4.55312 / 3.44 ( 585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.9138 (mmt) cc_final: 0.8844 (mmp) REVERT: A 159 LEU cc_start: 0.8412 (tt) cc_final: 0.7853 (mp) REVERT: A 264 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6818 (m-10) REVERT: A 371 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: A 438 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8290 (t80) outliers start: 18 outliers final: 7 residues processed: 82 average time/residue: 0.0314 time to fit residues: 3.7035 Evaluate side-chains 80 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 480 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.0040 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.0010 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.150305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122957 restraints weight = 6571.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126394 restraints weight = 3520.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128789 restraints weight = 2384.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129995 restraints weight = 1871.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130491 restraints weight = 1635.210| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3693 Z= 0.124 Angle : 0.603 9.538 5041 Z= 0.278 Chirality : 0.039 0.174 583 Planarity : 0.004 0.028 628 Dihedral : 10.261 178.906 514 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.94 % Allowed : 24.15 % Favored : 71.92 % 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: 1.07 (0.41), residues: 455 helix: 1.48 (0.30), residues: 308 sheet: -1.07 (1.48), residues: 10 loop : -0.85 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 162 TYR 0.008 0.001 TYR A 230 PHE 0.008 0.001 PHE A 185 TRP 0.012 0.001 TRP A 247 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 3691) covalent geometry : angle 0.60291 / 0.28 ( 5037) SS BOND : bond 0.00068 / 0.03 ( 2) SS BOND : angle 0.19890 / 0.12 ( 4) hydrogen bonds : bond 0.06155 / 4.14 ( 202) hydrogen bonds : angle 4.04535 / 3.06 ( 585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.9162 (mmt) cc_final: 0.8851 (tpp) REVERT: A 159 LEU cc_start: 0.8308 (tt) cc_final: 0.7829 (mp) REVERT: A 197 MET cc_start: 0.8447 (ttp) cc_final: 0.8246 (ttm) REVERT: A 212 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8337 (mm-30) REVERT: A 264 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6634 (m-10) REVERT: A 438 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8263 (t80) REVERT: A 442 PHE cc_start: 0.8253 (t80) cc_final: 0.7936 (t80) outliers start: 15 outliers final: 6 residues processed: 90 average time/residue: 0.0318 time to fit residues: 4.0904 Evaluate side-chains 80 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 480 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 205 ASN A 217 HIS ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.150014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123068 restraints weight = 6525.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126291 restraints weight = 3622.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128204 restraints weight = 2501.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129736 restraints weight = 2012.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.130063 restraints weight = 1747.898| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3693 Z= 0.126 Angle : 0.602 9.785 5041 Z= 0.276 Chirality : 0.040 0.144 583 Planarity : 0.004 0.025 628 Dihedral : 9.572 175.863 514 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.67 % Allowed : 26.25 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.41), residues: 455 helix: 1.60 (0.30), residues: 309 sheet: -1.17 (1.43), residues: 10 loop : -0.99 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 423 TYR 0.010 0.001 TYR A 230 PHE 0.008 0.001 PHE A 351 TRP 0.012 0.001 TRP A 247 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 3691) covalent geometry : angle 0.60242 / 0.28 ( 5037) SS BOND : bond 0.00054 / 0.03 ( 2) SS BOND : angle 0.29036 / 0.16 ( 4) hydrogen bonds : bond 0.05435 / 3.65 ( 202) hydrogen bonds : angle 3.84320 / 2.88 ( 585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 438 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8285 (t80) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.0360 time to fit residues: 4.2210 Evaluate side-chains 85 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.150844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123886 restraints weight = 6465.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127233 restraints weight = 3579.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129470 restraints weight = 2455.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130638 restraints weight = 1946.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.131598 restraints weight = 1704.150| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3693 Z= 0.120 Angle : 0.601 8.602 5041 Z= 0.276 Chirality : 0.040 0.161 583 Planarity : 0.004 0.029 628 Dihedral : 9.258 173.420 514 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.77 % Allowed : 24.41 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.41), residues: 455 helix: 1.58 (0.30), residues: 310 sheet: -1.09 (1.43), residues: 10 loop : -0.99 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 219 TYR 0.016 0.001 TYR A 490 PHE 0.008 0.001 PHE A 351 TRP 0.013 0.001 TRP A 247 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 3691) covalent geometry : angle 0.60098 / 0.28 ( 5037) SS BOND : bond 0.00068 / 0.03 ( 2) SS BOND : angle 0.27828 / 0.14 ( 4) hydrogen bonds : bond 0.05152 / 3.47 ( 202) hydrogen bonds : angle 3.76959 / 2.81 ( 585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 371 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: A 438 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8281 (t80) outliers start: 22 outliers final: 11 residues processed: 91 average time/residue: 0.0254 time to fit residues: 3.3096 Evaluate side-chains 87 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.150136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123311 restraints weight = 6540.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126630 restraints weight = 3624.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128615 restraints weight = 2490.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130206 restraints weight = 1990.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130909 restraints weight = 1715.480| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3693 Z= 0.126 Angle : 0.627 10.908 5041 Z= 0.285 Chirality : 0.041 0.199 583 Planarity : 0.004 0.027 628 Dihedral : 9.094 171.317 514 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.77 % Allowed : 26.25 % Favored : 67.98 % 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: 1.11 (0.41), residues: 455 helix: 1.55 (0.30), residues: 310 sheet: -1.17 (1.40), residues: 10 loop : -1.00 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 423 TYR 0.018 0.001 TYR A 490 PHE 0.009 0.001 PHE A 351 TRP 0.013 0.001 TRP A 247 HIS 0.002 0.000 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 3691) covalent geometry : angle 0.62723 / 0.29 ( 5037) SS BOND : bond 0.00069 / 0.03 ( 2) SS BOND : angle 0.27963 / 0.15 ( 4) hydrogen bonds : bond 0.05070 / 3.42 ( 202) hydrogen bonds : angle 3.76690 / 2.80 ( 585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 438 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8273 (t80) outliers start: 22 outliers final: 16 residues processed: 89 average time/residue: 0.0360 time to fit residues: 4.3458 Evaluate side-chains 92 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.151905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124970 restraints weight = 6670.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128378 restraints weight = 3680.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130672 restraints weight = 2512.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131781 restraints weight = 1973.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132593 restraints weight = 1728.816| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3693 Z= 0.113 Angle : 0.614 10.173 5041 Z= 0.278 Chirality : 0.041 0.171 583 Planarity : 0.004 0.027 628 Dihedral : 8.922 169.954 514 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.72 % Allowed : 28.35 % Favored : 66.93 % 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: 1.14 (0.41), residues: 455 helix: 1.57 (0.30), residues: 310 sheet: -1.30 (1.35), residues: 10 loop : -0.98 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 395 TYR 0.014 0.001 TYR A 490 PHE 0.008 0.001 PHE A 351 TRP 0.014 0.001 TRP A 247 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 3691) covalent geometry : angle 0.61409 / 0.28 ( 5037) SS BOND : bond 0.00090 / 0.04 ( 2) SS BOND : angle 0.27261 / 0.13 ( 4) hydrogen bonds : bond 0.04709 / 3.19 ( 202) hydrogen bonds : angle 3.63432 / 2.70 ( 585) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 371 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: A 438 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8259 (t80) outliers start: 18 outliers final: 11 residues processed: 87 average time/residue: 0.0284 time to fit residues: 3.5241 Evaluate side-chains 89 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 0.0870 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 25 optimal weight: 0.0070 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.0652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.155112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128575 restraints weight = 6545.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.132114 restraints weight = 3603.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134426 restraints weight = 2440.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.135732 restraints weight = 1911.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136656 restraints weight = 1655.351| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3693 Z= 0.113 Angle : 0.620 10.489 5041 Z= 0.277 Chirality : 0.040 0.176 583 Planarity : 0.003 0.025 628 Dihedral : 8.932 171.875 514 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.20 % Allowed : 29.40 % Favored : 66.40 % 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: 1.17 (0.41), residues: 455 helix: 1.58 (0.30), residues: 310 sheet: -1.38 (1.34), residues: 10 loop : -0.92 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 454 TYR 0.016 0.001 TYR A 490 PHE 0.006 0.001 PHE A 261 TRP 0.017 0.001 TRP A 247 HIS 0.002 0.000 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 ( 3691) covalent geometry : angle 0.62056 / 0.28 ( 5037) SS BOND : bond 0.00135 / 0.06 ( 2) SS BOND : angle 0.26045 / 0.11 ( 4) hydrogen bonds : bond 0.04104 / 2.74 ( 202) hydrogen bonds : angle 3.50638 / 2.62 ( 585) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 438 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8235 (t80) outliers start: 16 outliers final: 12 residues processed: 85 average time/residue: 0.0256 time to fit residues: 3.1420 Evaluate side-chains 89 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 480 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN A 337 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.152769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125706 restraints weight = 6470.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129054 restraints weight = 3642.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131360 restraints weight = 2511.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132548 restraints weight = 1974.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133514 restraints weight = 1727.514| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3693 Z= 0.115 Angle : 0.642 10.425 5041 Z= 0.286 Chirality : 0.040 0.170 583 Planarity : 0.003 0.026 628 Dihedral : 8.845 169.669 514 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.46 % Allowed : 28.87 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.41), residues: 455 helix: 1.62 (0.30), residues: 310 sheet: -1.23 (1.33), residues: 10 loop : -0.97 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.018 0.001 TYR A 490 PHE 0.009 0.001 PHE A 351 TRP 0.012 0.001 TRP A 523 HIS 0.001 0.000 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 3691) covalent geometry : angle 0.64257 / 0.29 ( 5037) SS BOND : bond 0.00070 / 0.03 ( 2) SS BOND : angle 0.26659 / 0.14 ( 4) hydrogen bonds : bond 0.04404 / 2.97 ( 202) hydrogen bonds : angle 3.52916 / 2.62 ( 585) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.121 Fit side-chains REVERT: A 438 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8233 (t80) outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 0.0269 time to fit residues: 3.3024 Evaluate side-chains 89 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 480 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.0070 chunk 42 optimal weight: 0.0980 chunk 5 optimal weight: 0.0000 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3202 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.155813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.129080 restraints weight = 6553.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132688 restraints weight = 3629.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135003 restraints weight = 2460.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136292 restraints weight = 1929.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137213 restraints weight = 1670.602| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3693 Z= 0.106 Angle : 0.653 10.621 5041 Z= 0.289 Chirality : 0.040 0.177 583 Planarity : 0.003 0.027 628 Dihedral : 8.825 170.398 514 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.15 % Allowed : 30.18 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.40), residues: 455 helix: 1.61 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -0.78 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 454 TYR 0.016 0.001 TYR A 490 PHE 0.009 0.001 PHE A 16 TRP 0.016 0.001 TRP A 247 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 ( 3691) covalent geometry : angle 0.65335 / 0.29 ( 5037) SS BOND : bond 0.00128 / 0.06 ( 2) SS BOND : angle 0.29503 / 0.12 ( 4) hydrogen bonds : bond 0.03981 / 2.67 ( 202) hydrogen bonds : angle 3.52947 / 2.62 ( 585) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.097 Fit side-chains REVERT: A 261 PHE cc_start: 0.7963 (m-80) cc_final: 0.7635 (m-80) REVERT: A 438 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8238 (t80) outliers start: 12 outliers final: 10 residues processed: 81 average time/residue: 0.0325 time to fit residues: 3.7416 Evaluate side-chains 86 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 480 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.153419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126451 restraints weight = 6442.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.129833 restraints weight = 3613.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132113 restraints weight = 2501.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133388 restraints weight = 1971.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134382 restraints weight = 1718.503| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3693 Z= 0.112 Angle : 0.661 12.334 5041 Z= 0.289 Chirality : 0.041 0.177 583 Planarity : 0.004 0.030 628 Dihedral : 8.755 168.437 514 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.94 % Allowed : 28.35 % Favored : 67.72 % 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: 1.25 (0.41), residues: 455 helix: 1.66 (0.30), residues: 310 sheet: -1.15 (1.29), residues: 10 loop : -0.96 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 336 TYR 0.016 0.001 TYR A 490 PHE 0.008 0.001 PHE A 351 TRP 0.012 0.001 TRP A 523 HIS 0.001 0.000 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 3691) covalent geometry : angle 0.66127 / 0.29 ( 5037) SS BOND : bond 0.00057 / 0.03 ( 2) SS BOND : angle 0.25247 / 0.12 ( 4) hydrogen bonds : bond 0.04265 / 2.86 ( 202) hydrogen bonds : angle 3.52657 / 2.61 ( 585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 642.23 seconds wall clock time: 11 minutes 43.10 seconds (703.10 seconds total)