Starting phenix.real_space_refine on Fri Aug 22 15:44:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fei_29028/08_2025/8fei_29028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fei_29028/08_2025/8fei_29028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fei_29028/08_2025/8fei_29028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fei_29028/08_2025/8fei_29028.map" model { file = "/net/cci-nas-00/data/ceres_data/8fei_29028/08_2025/8fei_29028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fei_29028/08_2025/8fei_29028.cif" } resolution = 3.0 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= -0.001 sd= 0.026 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 Fe 2 7.16 5 S 41 5.16 5 C 3242 2.51 5 N 901 2.21 5 O 1003 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5189 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5187 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 649} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.35, per 1000 atoms: 0.26 Number of scatterers: 5189 At special positions: 0 Unit cell: (63.356, 74.14, 105.144, 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) Fe 2 26.01 S 41 16.00 O 1003 8.00 N 901 7.00 C 3242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 45 " distance=2.04 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 36 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 171 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 242 " distance=2.02 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 371 " distance=2.01 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 680 " distance=2.02 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 643 " distance=2.03 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 513 " distance=2.03 Simple disulfide: pdb=" SG CYS A 570 " - pdb=" SG CYS A 584 " 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 213.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 39.8% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 removed outlier: 3.676A pdb=" N LEU A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.917A pdb=" N GLU A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.639A pdb=" N LEU A 109 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN A 110 " --> pdb=" O ASN A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 106 through 110' Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.839A pdb=" N ALA A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.513A pdb=" N ARG A 172 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.285A pdb=" N CYS A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 200 removed outlier: 3.647A pdb=" N PHE A 195 " --> pdb=" O TYR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 217 removed outlier: 3.691A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 258 through 275 removed outlier: 4.484A pdb=" N ASP A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 321 removed outlier: 3.682A pdb=" N LEU A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 333 removed outlier: 3.649A pdb=" N ALA A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.507A pdb=" N LYS A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.639A pdb=" N ILE A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 removed outlier: 3.725A pdb=" N TYR A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.985A pdb=" N GLY A 450 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 475 Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.727A pdb=" N LEU A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 600 through 616 removed outlier: 3.679A pdb=" N ILE A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 614 " --> pdb=" O ARG A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 668 removed outlier: 3.799A pdb=" N GLY A 658 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASP A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LYS A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.573A pdb=" N CYS A 680 " --> pdb=" O ILE A 676 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 11 removed outlier: 6.106A pdb=" N ILE A 7 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 37 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP A 9 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.686A pdb=" N ILE A 57 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 78 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 254 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET A 306 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.518A pdb=" N SER A 114 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 113 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE A 207 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N CYS A 115 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N LYS A 209 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 208 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA A 96 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.518A pdb=" N SER A 114 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 113 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE A 207 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N CYS A 115 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N LYS A 209 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 208 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 245 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 350 removed outlier: 5.662A pdb=" N ILE A 345 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N THR A 372 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP A 347 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 374 " --> pdb=" O TRP A 347 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 349 " --> pdb=" O VAL A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 394 removed outlier: 3.882A pdb=" N VAL A 392 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 594 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS A 643 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 541 removed outlier: 4.668A pdb=" N ALA A 435 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A 570 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ARG A 574 " --> pdb=" O CYS A 570 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 537 through 541 removed outlier: 3.732A pdb=" N ALA A 587 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 removed outlier: 7.349A pdb=" N SER A 453 " --> pdb=" O CYS A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 177 hydrogen bonds defined for protein. 510 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: 0.89 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1168 1.33 - 1.45: 1125 1.45 - 1.57: 2943 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 5288 Sorted by residual: bond pdb=" N ILE A 57 " pdb=" CA ILE A 57 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.03e+01 bond pdb=" N LEU A 299 " pdb=" CA LEU A 299 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N VAL A 596 " pdb=" CA VAL A 596 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.22e-02 6.72e+03 9.68e+00 bond pdb=" N LYS A 181 " pdb=" CA LYS A 181 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.85e+00 bond pdb=" N PHE A 300 " pdb=" CA PHE A 300 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.13e-02 7.83e+03 7.83e+00 ... (remaining 5283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 6738 1.84 - 3.68: 361 3.68 - 5.51: 37 5.51 - 7.35: 6 7.35 - 9.19: 1 Bond angle restraints: 7143 Sorted by residual: angle pdb=" O TYR A 191 " pdb=" C TYR A 191 " pdb=" N SER A 192 " ideal model delta sigma weight residual 122.07 116.43 5.64 1.03e+00 9.43e-01 3.00e+01 angle pdb=" CA TYR A 191 " pdb=" C TYR A 191 " pdb=" N SER A 192 " ideal model delta sigma weight residual 117.07 122.99 -5.92 1.14e+00 7.69e-01 2.69e+01 angle pdb=" C LEU A 635 " pdb=" N LEU A 636 " pdb=" CA LEU A 636 " ideal model delta sigma weight residual 121.54 130.73 -9.19 1.91e+00 2.74e-01 2.32e+01 angle pdb=" CA GLY A 190 " pdb=" C GLY A 190 " pdb=" N TYR A 191 " ideal model delta sigma weight residual 114.69 121.23 -6.54 1.43e+00 4.89e-01 2.09e+01 angle pdb=" CA GLY A 190 " pdb=" C GLY A 190 " pdb=" O GLY A 190 " ideal model delta sigma weight residual 122.57 118.47 4.10 9.20e-01 1.18e+00 1.98e+01 ... (remaining 7138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 2854 15.57 - 31.13: 272 31.13 - 46.70: 83 46.70 - 62.27: 13 62.27 - 77.83: 13 Dihedral angle restraints: 3235 sinusoidal: 1298 harmonic: 1937 Sorted by residual: dihedral pdb=" CB CYS A 171 " pdb=" SG CYS A 171 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual 93.00 160.73 -67.73 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS A 570 " pdb=" SG CYS A 570 " pdb=" SG CYS A 584 " pdb=" CB CYS A 584 " ideal model delta sinusoidal sigma weight residual -86.00 -143.26 57.26 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS A 421 " pdb=" SG CYS A 421 " pdb=" SG CYS A 643 " pdb=" CB CYS A 643 " ideal model delta sinusoidal sigma weight residual -86.00 -131.13 45.13 1 1.00e+01 1.00e-02 2.83e+01 ... (remaining 3232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 617 0.059 - 0.119: 135 0.119 - 0.178: 23 0.178 - 0.238: 4 0.238 - 0.297: 1 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA ILE A 57 " pdb=" N ILE A 57 " pdb=" C ILE A 57 " pdb=" CB ILE A 57 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA GLU A 370 " pdb=" N GLU A 370 " pdb=" C GLU A 370 " pdb=" CB GLU A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA VAL A 596 " pdb=" N VAL A 596 " pdb=" C VAL A 596 " pdb=" CB VAL A 596 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 777 not shown) Planarity restraints: 933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 190 " 0.014 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C GLY A 190 " -0.045 2.00e-02 2.50e+03 pdb=" O GLY A 190 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 191 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 292 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO A 293 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 298 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C LEU A 298 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 298 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 299 " -0.012 2.00e-02 2.50e+03 ... (remaining 930 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 6 2.21 - 2.88: 1985 2.88 - 3.56: 7083 3.56 - 4.23: 12448 4.23 - 4.90: 20680 Nonbonded interactions: 42202 Sorted by model distance: nonbonded pdb=" OH TYR A 191 " pdb="FE FE A 701 " model vdw 1.541 2.260 nonbonded pdb=" OD2 ASP A 395 " pdb="FE FE A 702 " model vdw 1.984 2.260 nonbonded pdb=" OH TYR A 524 " pdb="FE FE A 702 " model vdw 2.039 2.260 nonbonded pdb=" NE2 HIS A 250 " pdb="FE FE A 701 " model vdw 2.089 2.340 nonbonded pdb=" OH TYR A 92 " pdb="FE FE A 701 " model vdw 2.098 2.260 ... (remaining 42197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.007 0.039 5303 Z= 0.397 Angle : 0.917 9.190 7173 Z= 0.606 Chirality : 0.053 0.297 780 Planarity : 0.005 0.054 933 Dihedral : 13.997 77.834 1946 Min Nonbonded Distance : 1.541 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.18 % Allowed : 7.14 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -3.98 (0.24), residues: 670 helix: -3.97 (0.16), residues: 211 sheet: -2.64 (0.48), residues: 74 loop : -1.81 (0.26), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 460 TYR 0.020 0.002 TYR A 191 PHE 0.011 0.002 PHE A 645 TRP 0.008 0.001 TRP A 347 HIS 0.006 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00688 ( 5288) covalent geometry : angle 0.91376 ( 7143) SS BOND : bond 0.00651 ( 15) SS BOND : angle 1.45164 ( 30) hydrogen bonds : bond 0.28420 ( 169) hydrogen bonds : angle 9.58808 ( 510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.217 Fit side-chains REVERT: A 679 MET cc_start: 0.8740 (ppp) cc_final: 0.8540 (ppp) REVERT: A 684 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7789 (pp20) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.7039 time to fit residues: 26.3386 Evaluate side-chains 17 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 51 ASN A 63 GLN A 500 GLN A 541 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.058943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047401 restraints weight = 19157.534| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.42 r_work: 0.2759 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5303 Z= 0.140 Angle : 0.553 6.382 7173 Z= 0.297 Chirality : 0.041 0.156 780 Planarity : 0.004 0.033 933 Dihedral : 4.756 28.330 725 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.71 % Allowed : 10.54 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -2.24 (0.27), residues: 670 helix: -1.70 (0.28), residues: 208 sheet: -2.54 (0.46), residues: 84 loop : -1.00 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 497 TYR 0.011 0.001 TYR A 431 PHE 0.010 0.001 PHE A 195 TRP 0.010 0.001 TRP A 264 HIS 0.003 0.000 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5288) covalent geometry : angle 0.55196 ( 7143) SS BOND : bond 0.00237 ( 15) SS BOND : angle 0.74699 ( 30) hydrogen bonds : bond 0.04004 ( 169) hydrogen bonds : angle 5.93439 ( 510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.230 Fit side-chains REVERT: A 411 MET cc_start: 0.8974 (mtp) cc_final: 0.8394 (mmm) REVERT: A 684 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7747 (pp20) outliers start: 4 outliers final: 0 residues processed: 25 average time/residue: 0.5183 time to fit residues: 13.6997 Evaluate side-chains 17 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.060077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.048629 restraints weight = 18953.752| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.41 r_work: 0.2803 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5303 Z= 0.090 Angle : 0.476 8.025 7173 Z= 0.252 Chirality : 0.039 0.118 780 Planarity : 0.003 0.027 933 Dihedral : 4.164 16.818 723 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.54 % Allowed : 11.07 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -1.43 (0.29), residues: 670 helix: -0.55 (0.32), residues: 210 sheet: -2.39 (0.47), residues: 84 loop : -0.74 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 497 TYR 0.009 0.001 TYR A 431 PHE 0.009 0.001 PHE A 300 TRP 0.006 0.001 TRP A 264 HIS 0.002 0.000 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 5288) covalent geometry : angle 0.47551 ( 7143) SS BOND : bond 0.00169 ( 15) SS BOND : angle 0.62543 ( 30) hydrogen bonds : bond 0.03084 ( 169) hydrogen bonds : angle 5.28416 ( 510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.144 Fit side-chains REVERT: A 306 MET cc_start: 0.8935 (tpt) cc_final: 0.8681 (tpp) REVERT: A 684 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7599 (pp20) outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 0.5762 time to fit residues: 13.4274 Evaluate side-chains 17 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.047457 restraints weight = 19319.283| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 4.41 r_work: 0.2752 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5303 Z= 0.137 Angle : 0.487 6.476 7173 Z= 0.258 Chirality : 0.040 0.142 780 Planarity : 0.003 0.026 933 Dihedral : 4.123 16.305 723 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.25 % Allowed : 10.71 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.91 (0.30), residues: 670 helix: 0.08 (0.34), residues: 212 sheet: -2.35 (0.47), residues: 84 loop : -0.47 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.011 0.001 TYR A 431 PHE 0.023 0.001 PHE A 266 TRP 0.009 0.001 TRP A 347 HIS 0.002 0.000 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5288) covalent geometry : angle 0.48628 ( 7143) SS BOND : bond 0.00259 ( 15) SS BOND : angle 0.60481 ( 30) hydrogen bonds : bond 0.03127 ( 169) hydrogen bonds : angle 5.14566 ( 510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.225 Fit side-chains REVERT: A 306 MET cc_start: 0.8999 (tpt) cc_final: 0.8773 (tpp) REVERT: A 626 MET cc_start: 0.8344 (mmm) cc_final: 0.8073 (tpp) REVERT: A 684 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7661 (pp20) outliers start: 7 outliers final: 3 residues processed: 22 average time/residue: 0.5448 time to fit residues: 12.7264 Evaluate side-chains 20 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 57 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.060100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.048375 restraints weight = 19634.793| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.53 r_work: 0.2784 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5303 Z= 0.084 Angle : 0.447 8.392 7173 Z= 0.236 Chirality : 0.039 0.116 780 Planarity : 0.003 0.025 933 Dihedral : 3.901 15.718 723 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.89 % Allowed : 11.43 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.67 (0.31), residues: 670 helix: 0.38 (0.36), residues: 212 sheet: -2.24 (0.48), residues: 84 loop : -0.39 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 597 TYR 0.011 0.001 TYR A 431 PHE 0.010 0.001 PHE A 266 TRP 0.005 0.001 TRP A 264 HIS 0.002 0.000 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 5288) covalent geometry : angle 0.44668 ( 7143) SS BOND : bond 0.00178 ( 15) SS BOND : angle 0.51205 ( 30) hydrogen bonds : bond 0.02673 ( 169) hydrogen bonds : angle 4.98090 ( 510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.210 Fit side-chains REVERT: A 306 MET cc_start: 0.8930 (tpt) cc_final: 0.8724 (tpp) REVERT: A 626 MET cc_start: 0.8303 (mmm) cc_final: 0.8095 (tpp) REVERT: A 684 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7632 (pp20) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 0.5493 time to fit residues: 12.8225 Evaluate side-chains 19 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.058224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046642 restraints weight = 19605.654| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 4.40 r_work: 0.2729 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5303 Z= 0.185 Angle : 0.528 9.289 7173 Z= 0.277 Chirality : 0.041 0.136 780 Planarity : 0.003 0.025 933 Dihedral : 4.119 16.318 723 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.89 % Allowed : 12.14 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.39 (0.32), residues: 670 helix: 0.67 (0.37), residues: 211 sheet: -2.26 (0.48), residues: 84 loop : -0.21 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.011 0.001 TYR A 191 PHE 0.026 0.001 PHE A 266 TRP 0.011 0.001 TRP A 347 HIS 0.002 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 5288) covalent geometry : angle 0.52748 ( 7143) SS BOND : bond 0.00308 ( 15) SS BOND : angle 0.59507 ( 30) hydrogen bonds : bond 0.03192 ( 169) hydrogen bonds : angle 5.08853 ( 510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.237 Fit side-chains REVERT: A 306 MET cc_start: 0.9000 (tpt) cc_final: 0.8750 (tpp) REVERT: A 626 MET cc_start: 0.8414 (mmm) cc_final: 0.7829 (tpp) REVERT: A 684 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7768 (pp20) outliers start: 5 outliers final: 3 residues processed: 21 average time/residue: 0.4709 time to fit residues: 10.5929 Evaluate side-chains 19 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 0.0670 chunk 1 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.060220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.048524 restraints weight = 19316.476| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.47 r_work: 0.2772 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5303 Z= 0.094 Angle : 0.471 10.245 7173 Z= 0.244 Chirality : 0.039 0.115 780 Planarity : 0.003 0.025 933 Dihedral : 3.905 15.522 723 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.07 % Allowed : 12.14 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.30 (0.32), residues: 670 helix: 0.77 (0.37), residues: 212 sheet: -2.14 (0.49), residues: 84 loop : -0.20 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 460 TYR 0.011 0.001 TYR A 431 PHE 0.008 0.001 PHE A 645 TRP 0.005 0.001 TRP A 125 HIS 0.002 0.000 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 5288) covalent geometry : angle 0.47096 ( 7143) SS BOND : bond 0.00197 ( 15) SS BOND : angle 0.47960 ( 30) hydrogen bonds : bond 0.02626 ( 169) hydrogen bonds : angle 4.93265 ( 510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.163 Fit side-chains REVERT: A 306 MET cc_start: 0.8917 (tpt) cc_final: 0.8687 (tpp) REVERT: A 626 MET cc_start: 0.8309 (mmm) cc_final: 0.7672 (tpp) REVERT: A 684 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7681 (pp20) outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 0.5286 time to fit residues: 13.9801 Evaluate side-chains 22 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.060239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.048602 restraints weight = 19144.161| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.43 r_work: 0.2776 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5303 Z= 0.101 Angle : 0.501 11.123 7173 Z= 0.256 Chirality : 0.040 0.115 780 Planarity : 0.003 0.025 933 Dihedral : 3.862 15.386 723 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.54 % Allowed : 14.11 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.22 (0.33), residues: 670 helix: 0.88 (0.37), residues: 212 sheet: -2.20 (0.49), residues: 87 loop : -0.11 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 460 TYR 0.010 0.001 TYR A 431 PHE 0.031 0.001 PHE A 266 TRP 0.005 0.001 TRP A 264 HIS 0.002 0.000 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 5288) covalent geometry : angle 0.50085 ( 7143) SS BOND : bond 0.00196 ( 15) SS BOND : angle 0.48096 ( 30) hydrogen bonds : bond 0.02628 ( 169) hydrogen bonds : angle 4.89482 ( 510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.221 Fit side-chains REVERT: A 306 MET cc_start: 0.8914 (tpt) cc_final: 0.8688 (tpp) REVERT: A 626 MET cc_start: 0.8276 (mmm) cc_final: 0.7688 (tpp) REVERT: A 684 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7699 (pp20) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.6123 time to fit residues: 14.2308 Evaluate side-chains 20 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.0170 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.060432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.048882 restraints weight = 19216.659| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.42 r_work: 0.2810 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5303 Z= 0.089 Angle : 0.504 11.836 7173 Z= 0.257 Chirality : 0.039 0.134 780 Planarity : 0.003 0.025 933 Dihedral : 3.732 15.052 723 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.71 % Allowed : 14.46 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.15 (0.32), residues: 670 helix: 0.96 (0.37), residues: 212 sheet: -2.12 (0.49), residues: 87 loop : -0.10 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 605 TYR 0.009 0.001 TYR A 431 PHE 0.025 0.001 PHE A 300 TRP 0.004 0.001 TRP A 264 HIS 0.002 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 5288) covalent geometry : angle 0.50468 ( 7143) SS BOND : bond 0.00166 ( 15) SS BOND : angle 0.44855 ( 30) hydrogen bonds : bond 0.02428 ( 169) hydrogen bonds : angle 4.82773 ( 510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.215 Fit side-chains REVERT: A 306 MET cc_start: 0.8941 (tpt) cc_final: 0.8719 (tpp) REVERT: A 626 MET cc_start: 0.8095 (mmm) cc_final: 0.7590 (tpp) REVERT: A 684 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7675 (pp20) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.4904 time to fit residues: 12.0360 Evaluate side-chains 19 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 0 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.060739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.049149 restraints weight = 19090.820| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 4.42 r_work: 0.2794 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5303 Z= 0.099 Angle : 0.519 12.213 7173 Z= 0.264 Chirality : 0.039 0.127 780 Planarity : 0.003 0.025 933 Dihedral : 3.764 15.030 723 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.54 % Allowed : 14.82 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.01 (0.33), residues: 670 helix: 1.05 (0.37), residues: 212 sheet: -1.88 (0.52), residues: 77 loop : -0.11 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 460 TYR 0.009 0.001 TYR A 431 PHE 0.044 0.002 PHE A 300 TRP 0.005 0.001 TRP A 264 HIS 0.002 0.000 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 5288) covalent geometry : angle 0.51889 ( 7143) SS BOND : bond 0.00178 ( 15) SS BOND : angle 0.43971 ( 30) hydrogen bonds : bond 0.02467 ( 169) hydrogen bonds : angle 4.82258 ( 510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.191 Fit side-chains REVERT: A 306 MET cc_start: 0.8914 (tpt) cc_final: 0.8673 (tpp) REVERT: A 376 GLU cc_start: 0.8929 (mp0) cc_final: 0.8502 (tt0) REVERT: A 626 MET cc_start: 0.8053 (mmm) cc_final: 0.7574 (tpp) REVERT: A 684 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7696 (pp20) outliers start: 3 outliers final: 3 residues processed: 19 average time/residue: 0.5514 time to fit residues: 11.1709 Evaluate side-chains 18 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.0270 chunk 45 optimal weight: 5.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.060345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.048940 restraints weight = 19243.376| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.37 r_work: 0.2816 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5303 Z= 0.096 Angle : 0.523 12.238 7173 Z= 0.264 Chirality : 0.039 0.124 780 Planarity : 0.003 0.025 933 Dihedral : 3.730 15.594 723 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.54 % Allowed : 14.82 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.05 (0.33), residues: 670 helix: 1.12 (0.37), residues: 212 sheet: -1.85 (0.53), residues: 77 loop : -0.08 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 460 TYR 0.009 0.001 TYR A 431 PHE 0.045 0.001 PHE A 300 TRP 0.005 0.001 TRP A 264 HIS 0.002 0.000 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 5288) covalent geometry : angle 0.52286 ( 7143) SS BOND : bond 0.00175 ( 15) SS BOND : angle 0.43141 ( 30) hydrogen bonds : bond 0.02376 ( 169) hydrogen bonds : angle 4.79836 ( 510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1367.88 seconds wall clock time: 24 minutes 12.52 seconds (1452.52 seconds total)