Starting phenix.real_space_refine on Tue Feb 3 14:23:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9klz_62418/02_2026/9klz_62418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9klz_62418/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9klz_62418/02_2026/9klz_62418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9klz_62418/02_2026/9klz_62418.map" model { file = "/net/cci-nas-00/data/ceres_data/9klz_62418/02_2026/9klz_62418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9klz_62418/02_2026/9klz_62418.cif" } 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-2.0-5952/lib/python3.9/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, 34 Unusual residues: {' CL': 1, 'OLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.01, 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: 0.31 Conformation dependent library (CDL) restraints added in 138.4 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: 0.13 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: 0.52 Time building geometry restraints manager: 0.41 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: 1.290 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.690 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 covalent geometry : bond 0.00394 ( 3691) covalent geometry : angle 0.64038 ( 5037) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.69755 ( 4) hydrogen bonds : bond 0.32548 ( 202) hydrogen bonds : angle 7.06243 ( 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 : 0.136 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: 0.0370 time to fit residues: 3.5601 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 : 0.143 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3849 r_free = 0.3849 target = 0.145565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116856 restraints weight = 6959.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.120469 restraints weight = 3655.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122876 restraints weight = 2437.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124117 restraints weight = 1899.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125098 restraints weight = 1657.632| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1611 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= 0.158 Angle : 0.642 9.618 5041 Z= 0.312 Chirality : 0.040 0.127 583 Planarity : 0.004 0.030 628 Dihedral : 10.836 175.887 514 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.72 % Allowed : 25.46 % 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: 0.97 (0.41), residues: 455 helix: 1.34 (0.30), residues: 305 sheet: -1.02 (1.51), residues: 10 loop : -0.69 (0.56), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 423 TYR 0.012 0.001 TYR A 490 PHE 0.009 0.001 PHE A 386 TRP 0.013 0.001 TRP A 346 HIS 0.002 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3691) covalent geometry : angle 0.64247 ( 5037) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.33333 ( 4) hydrogen bonds : bond 0.08149 ( 202) hydrogen bonds : angle 4.56619 ( 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 : 0.132 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.9138 (mmt) cc_final: 0.8845 (mmp) REVERT: A 159 LEU cc_start: 0.8411 (tt) cc_final: 0.7850 (mp) REVERT: A 264 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6820 (m-10) REVERT: A 371 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: A 438 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8289 (t80) outliers start: 18 outliers final: 7 residues processed: 82 average time/residue: 0.0384 time to fit residues: 4.4762 Evaluate side-chains 81 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 39 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 337 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.147393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119739 restraints weight = 6607.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123153 restraints weight = 3581.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125480 restraints weight = 2429.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126729 restraints weight = 1908.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127064 restraints weight = 1670.260| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3693 Z= 0.149 Angle : 0.632 9.493 5041 Z= 0.297 Chirality : 0.040 0.164 583 Planarity : 0.004 0.028 628 Dihedral : 10.490 179.065 514 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.94 % Allowed : 25.20 % Favored : 70.87 % 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: 1.04 (0.41), residues: 455 helix: 1.48 (0.30), residues: 306 sheet: -1.03 (1.50), residues: 10 loop : -0.91 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 162 TYR 0.011 0.001 TYR A 230 PHE 0.010 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 covalent geometry : bond 0.00311 ( 3691) covalent geometry : angle 0.63187 ( 5037) SS BOND : bond 0.00059 ( 2) SS BOND : angle 0.29045 ( 4) hydrogen bonds : bond 0.06703 ( 202) hydrogen bonds : angle 4.20694 ( 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 93 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8367 (tt) cc_final: 0.7877 (mp) REVERT: A 212 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8377 (mm-30) REVERT: A 264 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6795 (m-10) REVERT: A 438 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8318 (t80) outliers start: 15 outliers final: 6 residues processed: 87 average time/residue: 0.0379 time to fit residues: 4.6833 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 : 0.134 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 205 ASN A 371 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.147628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119994 restraints weight = 6567.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123424 restraints weight = 3552.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125746 restraints weight = 2406.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.126917 restraints weight = 1886.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127912 restraints weight = 1653.082| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2176 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= 0.146 Angle : 0.630 10.032 5041 Z= 0.294 Chirality : 0.040 0.153 583 Planarity : 0.004 0.026 628 Dihedral : 9.905 174.675 514 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.99 % Allowed : 24.67 % Favored : 70.34 % 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: 1.01 (0.41), residues: 455 helix: 1.47 (0.30), residues: 309 sheet: -1.04 (1.46), residues: 10 loop : -1.03 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 280 TYR 0.015 0.001 TYR A 490 PHE 0.010 0.001 PHE A 351 TRP 0.014 0.001 TRP A 247 HIS 0.002 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3691) covalent geometry : angle 0.63059 ( 5037) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.31265 ( 4) hydrogen bonds : bond 0.06041 ( 202) hydrogen bonds : angle 4.03869 ( 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 95 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.9167 (mmt) cc_final: 0.8892 (mmp) REVERT: A 184 ASN cc_start: 0.8253 (m-40) cc_final: 0.7147 (t0) REVERT: A 371 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: A 438 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8331 (t80) outliers start: 19 outliers final: 11 residues processed: 88 average time/residue: 0.0324 time to fit residues: 4.0108 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 : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 480 GLU Chi-restraints excluded: chain A residue 489 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.147864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120648 restraints weight = 6587.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124156 restraints weight = 3539.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126438 restraints weight = 2376.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127650 restraints weight = 1861.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128626 restraints weight = 1626.589| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3693 Z= 0.136 Angle : 0.616 8.803 5041 Z= 0.289 Chirality : 0.041 0.158 583 Planarity : 0.004 0.028 628 Dihedral : 9.489 172.201 514 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.99 % Allowed : 24.93 % 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: 1.04 (0.41), residues: 455 helix: 1.52 (0.30), residues: 308 sheet: -1.12 (1.44), residues: 10 loop : -1.05 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 162 TYR 0.017 0.001 TYR A 490 PHE 0.010 0.001 PHE A 351 TRP 0.015 0.001 TRP A 247 HIS 0.002 0.000 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3691) covalent geometry : angle 0.61623 ( 5037) SS BOND : bond 0.00066 ( 2) SS BOND : angle 0.29593 ( 4) hydrogen bonds : bond 0.05625 ( 202) hydrogen bonds : angle 3.96287 ( 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 97 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 438 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8335 (t80) outliers start: 19 outliers final: 13 residues processed: 88 average time/residue: 0.0320 time to fit residues: 4.0300 Evaluate side-chains 87 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 VAL 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 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 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 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 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.149401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122038 restraints weight = 6656.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125645 restraints weight = 3583.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127727 restraints weight = 2405.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129357 restraints weight = 1904.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130107 restraints weight = 1635.786| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3693 Z= 0.122 Angle : 0.625 10.984 5041 Z= 0.286 Chirality : 0.040 0.190 583 Planarity : 0.004 0.026 628 Dihedral : 9.131 170.743 514 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.99 % Allowed : 26.25 % Favored : 68.77 % 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: 1.09 (0.41), residues: 455 helix: 1.53 (0.30), residues: 311 sheet: -1.23 (1.38), residues: 10 loop : -1.00 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 423 TYR 0.014 0.001 TYR A 490 PHE 0.009 0.001 PHE A 351 TRP 0.016 0.001 TRP A 247 HIS 0.002 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3691) covalent geometry : angle 0.62474 ( 5037) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.26829 ( 4) hydrogen bonds : bond 0.05120 ( 202) hydrogen bonds : angle 3.80556 ( 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 93 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.089 Fit side-chains REVERT: A 371 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: A 438 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8312 (t80) outliers start: 19 outliers final: 14 residues processed: 84 average time/residue: 0.0438 time to fit residues: 4.9788 Evaluate side-chains 89 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 140 LEU 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 421 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR 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: 0.7980 chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.0010 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124447 restraints weight = 6732.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127876 restraints weight = 3689.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130203 restraints weight = 2505.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131434 restraints weight = 1967.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132323 restraints weight = 1709.852| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3693 Z= 0.115 Angle : 0.618 10.248 5041 Z= 0.284 Chirality : 0.040 0.171 583 Planarity : 0.004 0.028 628 Dihedral : 9.023 170.426 514 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.25 % Allowed : 26.25 % Favored : 68.50 % 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: 311 sheet: -1.28 (1.36), residues: 10 loop : -0.99 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.018 0.001 TYR A 490 PHE 0.007 0.001 PHE A 351 TRP 0.016 0.001 TRP A 247 HIS 0.002 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 3691) covalent geometry : angle 0.61796 ( 5037) SS BOND : bond 0.00089 ( 2) SS BOND : angle 0.24142 ( 4) hydrogen bonds : bond 0.04829 ( 202) hydrogen bonds : angle 3.74290 ( 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: 20 poor density : 76 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: A 438 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8267 (t80) outliers start: 20 outliers final: 13 residues processed: 87 average time/residue: 0.0376 time to fit residues: 4.6666 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 : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 140 LEU 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 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 440 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 460 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.151804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125082 restraints weight = 6606.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128537 restraints weight = 3624.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130636 restraints weight = 2460.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132221 restraints weight = 1948.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133018 restraints weight = 1677.748| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3693 Z= 0.115 Angle : 0.641 10.432 5041 Z= 0.290 Chirality : 0.041 0.177 583 Planarity : 0.003 0.027 628 Dihedral : 8.918 169.250 514 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.46 % Allowed : 28.08 % Favored : 67.45 % 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: 1.13 (0.41), residues: 455 helix: 1.56 (0.30), residues: 311 sheet: -1.30 (1.35), residues: 10 loop : -0.98 (0.56), residues: 134 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 0.008 0.001 PHE A 351 TRP 0.015 0.001 TRP A 247 HIS 0.001 0.000 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3691) covalent geometry : angle 0.64169 ( 5037) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.25726 ( 4) hydrogen bonds : bond 0.04716 ( 202) hydrogen bonds : angle 3.67884 ( 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 94 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 438 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8260 (t80) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 0.0377 time to fit residues: 4.6926 Evaluate side-chains 88 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE 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 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 440 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.150837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124183 restraints weight = 6428.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127590 restraints weight = 3575.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129571 restraints weight = 2439.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131072 restraints weight = 1944.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131733 restraints weight = 1699.313| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3693 Z= 0.125 Angle : 0.662 10.537 5041 Z= 0.298 Chirality : 0.041 0.179 583 Planarity : 0.004 0.027 628 Dihedral : 8.742 164.343 514 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.72 % Allowed : 28.08 % Favored : 67.19 % 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: 1.51 (0.30), residues: 311 sheet: -1.19 (1.35), residues: 10 loop : -1.00 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 15 TYR 0.019 0.001 TYR A 490 PHE 0.009 0.001 PHE A 351 TRP 0.014 0.001 TRP A 247 HIS 0.001 0.000 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3691) covalent geometry : angle 0.66253 ( 5037) SS BOND : bond 0.00066 ( 2) SS BOND : angle 0.29119 ( 4) hydrogen bonds : bond 0.04800 ( 202) hydrogen bonds : angle 3.73189 ( 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 94 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 438 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8261 (t80) outliers start: 18 outliers final: 16 residues processed: 86 average time/residue: 0.0264 time to fit residues: 3.2277 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 : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 140 LEU 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 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 440 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 460 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.153081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126523 restraints weight = 6592.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130033 restraints weight = 3623.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132118 restraints weight = 2456.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133804 restraints weight = 1939.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134535 restraints weight = 1656.077| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3081 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= 0.114 Angle : 0.663 10.925 5041 Z= 0.299 Chirality : 0.040 0.192 583 Planarity : 0.004 0.026 628 Dihedral : 8.671 163.676 514 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.41 % Allowed : 29.13 % Favored : 67.45 % 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: 1.54 (0.30), residues: 310 sheet: -1.40 (1.24), residues: 10 loop : -0.96 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 273 TYR 0.019 0.001 TYR A 490 PHE 0.008 0.001 PHE A 351 TRP 0.018 0.001 TRP A 247 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 3691) covalent geometry : angle 0.66325 ( 5037) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.29097 ( 4) hydrogen bonds : bond 0.04342 ( 202) hydrogen bonds : angle 3.64374 ( 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 86 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.138 Fit side-chains REVERT: A 438 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8303 (t80) outliers start: 13 outliers final: 9 residues processed: 78 average time/residue: 0.0395 time to fit residues: 4.3762 Evaluate side-chains 84 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE 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 438 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.150447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123688 restraints weight = 6453.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127007 restraints weight = 3629.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129158 restraints weight = 2498.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130354 restraints weight = 1981.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131183 restraints weight = 1733.357| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3693 Z= 0.133 Angle : 0.667 10.771 5041 Z= 0.302 Chirality : 0.041 0.185 583 Planarity : 0.004 0.030 628 Dihedral : 8.569 160.573 514 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.94 % Allowed : 28.08 % 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: 1.13 (0.41), residues: 455 helix: 1.54 (0.30), residues: 310 sheet: -1.35 (1.23), residues: 10 loop : -0.90 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 466 TYR 0.020 0.002 TYR A 353 PHE 0.011 0.001 PHE A 351 TRP 0.012 0.001 TRP A 523 HIS 0.004 0.000 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3691) covalent geometry : angle 0.66747 ( 5037) SS BOND : bond 0.00044 ( 2) SS BOND : angle 0.25945 ( 4) hydrogen bonds : bond 0.04879 ( 202) hydrogen bonds : angle 3.74149 ( 585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 709.33 seconds wall clock time: 12 minutes 51.92 seconds (771.92 seconds total)