Starting phenix.real_space_refine on Thu Jun 5 04:58:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fei_29028/06_2025/8fei_29028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fei_29028/06_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_29028/06_2025/8fei_29028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fei_29028/06_2025/8fei_29028.map" model { file = "/net/cci-nas-00/data/ceres_data/8fei_29028/06_2025/8fei_29028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fei_29028/06_2025/8fei_29028.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.34, per 1000 atoms: 1.03 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: 1.58 Conformation dependent library (CDL) restraints added in 687.1 milliseconds 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: 0.83 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: 3.27 Time building geometry restraints manager: 1.59 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: 38.310 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.520 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:19.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.090 ------------------------------------------------------------------------------- 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 : 5.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 347 HIS 0.006 0.001 HIS A 210 PHE 0.011 0.002 PHE A 645 TYR 0.020 0.002 TYR A 191 ARG 0.004 0.001 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.28420 ( 169) hydrogen bonds : angle 9.58808 ( 510) SS BOND : bond 0.00651 ( 15) SS BOND : angle 1.45164 ( 30) covalent geometry : bond 0.00688 ( 5288) covalent geometry : angle 0.91376 ( 7143) *********************** 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 : 0.589 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: 2.1988 time to fit residues: 82.0920 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 : 0.838 ------------------------------------------------------------------------------- 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 56 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3231 r_free = 0.3231 target = 0.057623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.045932 restraints weight = 19475.163| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 4.37 r_work: 0.2723 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5303 Z= 0.244 Angle : 0.619 6.093 7173 Z= 0.331 Chirality : 0.043 0.177 780 Planarity : 0.004 0.034 933 Dihedral : 4.966 29.409 725 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.25 % Allowed : 10.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.28), residues: 670 helix: -1.61 (0.29), residues: 210 sheet: -2.69 (0.44), residues: 84 loop : -0.90 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 264 HIS 0.003 0.001 HIS A 542 PHE 0.009 0.001 PHE A 195 TYR 0.012 0.002 TYR A 431 ARG 0.006 0.001 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 169) hydrogen bonds : angle 5.93125 ( 510) SS BOND : bond 0.00391 ( 15) SS BOND : angle 0.85536 ( 30) covalent geometry : bond 0.00550 ( 5288) covalent geometry : angle 0.61766 ( 7143) *********************** 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 26 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.654 Fit side-chains REVERT: A 684 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7729 (pp20) outliers start: 7 outliers final: 1 residues processed: 25 average time/residue: 1.6860 time to fit residues: 45.0271 Evaluate side-chains 19 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 12 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.059239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047329 restraints weight = 18820.527| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.43 r_work: 0.2777 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5303 Z= 0.091 Angle : 0.480 7.511 7173 Z= 0.254 Chirality : 0.039 0.121 780 Planarity : 0.003 0.028 933 Dihedral : 4.252 16.740 723 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.07 % Allowed : 10.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.29), residues: 670 helix: -0.50 (0.32), residues: 210 sheet: -2.49 (0.46), residues: 84 loop : -0.66 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 445 HIS 0.002 0.000 HIS A 196 PHE 0.008 0.001 PHE A 645 TYR 0.009 0.001 TYR A 431 ARG 0.003 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 169) hydrogen bonds : angle 5.33679 ( 510) SS BOND : bond 0.00193 ( 15) SS BOND : angle 0.59462 ( 30) covalent geometry : bond 0.00204 ( 5288) covalent geometry : angle 0.47947 ( 7143) *********************** 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 27 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.568 Fit side-chains REVERT: A 306 MET cc_start: 0.8956 (tpt) cc_final: 0.8708 (tpp) REVERT: A 588 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: A 684 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7660 (pp20) outliers start: 6 outliers final: 1 residues processed: 26 average time/residue: 1.1941 time to fit residues: 33.0356 Evaluate side-chains 20 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 588 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.058495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046912 restraints weight = 19747.442| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 4.41 r_work: 0.2740 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5303 Z= 0.157 Angle : 0.510 7.612 7173 Z= 0.269 Chirality : 0.041 0.133 780 Planarity : 0.003 0.027 933 Dihedral : 4.258 16.111 723 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.43 % Allowed : 10.36 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.31), residues: 670 helix: 0.13 (0.35), residues: 211 sheet: -2.44 (0.46), residues: 84 loop : -0.43 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 347 HIS 0.002 0.000 HIS A 196 PHE 0.022 0.001 PHE A 266 TYR 0.012 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 169) hydrogen bonds : angle 5.21435 ( 510) SS BOND : bond 0.00276 ( 15) SS BOND : angle 0.63598 ( 30) covalent geometry : bond 0.00358 ( 5288) covalent geometry : angle 0.50916 ( 7143) *********************** 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 25 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.635 Fit side-chains REVERT: A 306 MET cc_start: 0.8997 (tpt) cc_final: 0.8737 (tpp) REVERT: A 626 MET cc_start: 0.8363 (mmm) cc_final: 0.8072 (tpp) REVERT: A 684 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7748 (pp20) outliers start: 8 outliers final: 4 residues processed: 23 average time/residue: 1.2834 time to fit residues: 31.5543 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 : 0.646 ------------------------------------------------------------------------------- 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 627 MET 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 47 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.058791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.047134 restraints weight = 19555.957| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.40 r_work: 0.2749 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5303 Z= 0.124 Angle : 0.479 8.256 7173 Z= 0.253 Chirality : 0.040 0.118 780 Planarity : 0.003 0.026 933 Dihedral : 4.146 15.761 723 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.54 % Allowed : 12.14 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.31), residues: 670 helix: 0.47 (0.36), residues: 211 sheet: -2.30 (0.47), residues: 84 loop : -0.33 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 347 HIS 0.002 0.000 HIS A 196 PHE 0.008 0.001 PHE A 645 TYR 0.012 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 169) hydrogen bonds : angle 5.10759 ( 510) SS BOND : bond 0.00240 ( 15) SS BOND : angle 0.54821 ( 30) covalent geometry : bond 0.00285 ( 5288) covalent geometry : angle 0.47838 ( 7143) *********************** 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 21 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.633 Fit side-chains REVERT: A 306 MET cc_start: 0.8949 (tpt) cc_final: 0.8699 (tpp) REVERT: A 626 MET cc_start: 0.8432 (mmm) cc_final: 0.8194 (tpp) REVERT: A 684 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7727 (pp20) outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 1.3412 time to fit residues: 30.0972 Evaluate side-chains 19 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 48 optimal weight: 0.0770 overall best weight: 1.3342 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.058694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.047134 restraints weight = 19386.347| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.38 r_work: 0.2746 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2422 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= 0.124 Angle : 0.487 9.323 7173 Z= 0.256 Chirality : 0.040 0.117 780 Planarity : 0.003 0.026 933 Dihedral : 4.103 15.687 723 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.07 % Allowed : 12.86 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.32), residues: 670 helix: 0.62 (0.36), residues: 212 sheet: -2.22 (0.48), residues: 84 loop : -0.22 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 347 HIS 0.002 0.000 HIS A 196 PHE 0.027 0.001 PHE A 266 TYR 0.011 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 169) hydrogen bonds : angle 5.04344 ( 510) SS BOND : bond 0.00243 ( 15) SS BOND : angle 0.53762 ( 30) covalent geometry : bond 0.00286 ( 5288) covalent geometry : angle 0.48711 ( 7143) *********************** 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 23 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.587 Fit side-chains REVERT: A 306 MET cc_start: 0.8998 (tpt) cc_final: 0.8749 (tpp) REVERT: A 626 MET cc_start: 0.8426 (mmm) cc_final: 0.7807 (tpp) REVERT: A 684 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7781 (pp20) outliers start: 6 outliers final: 3 residues processed: 23 average time/residue: 1.2583 time to fit residues: 30.9271 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 : 0.771 ------------------------------------------------------------------------------- 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 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.058724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.047279 restraints weight = 19054.847| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.33 r_work: 0.2765 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5303 Z= 0.124 Angle : 0.493 10.309 7173 Z= 0.257 Chirality : 0.040 0.118 780 Planarity : 0.003 0.026 933 Dihedral : 4.066 15.751 723 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.25 % Allowed : 13.04 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.32), residues: 670 helix: 0.74 (0.37), residues: 211 sheet: -2.17 (0.49), residues: 84 loop : -0.18 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 347 HIS 0.002 0.000 HIS A 196 PHE 0.008 0.001 PHE A 645 TYR 0.011 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.02869 ( 169) hydrogen bonds : angle 5.02095 ( 510) SS BOND : bond 0.00239 ( 15) SS BOND : angle 0.51861 ( 30) covalent geometry : bond 0.00287 ( 5288) covalent geometry : angle 0.49287 ( 7143) *********************** 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 24 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.599 Fit side-chains REVERT: A 306 MET cc_start: 0.8956 (tpt) cc_final: 0.8602 (tpt) REVERT: A 626 MET cc_start: 0.8357 (mmm) cc_final: 0.7805 (tpp) REVERT: A 684 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7797 (pp20) outliers start: 7 outliers final: 3 residues processed: 24 average time/residue: 1.1509 time to fit residues: 29.6209 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 : 0.590 ------------------------------------------------------------------------------- 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 48 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.1080 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.059037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.047557 restraints weight = 19185.433| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.34 r_work: 0.2777 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2573 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= 0.110 Angle : 0.498 11.015 7173 Z= 0.255 Chirality : 0.040 0.130 780 Planarity : 0.003 0.026 933 Dihedral : 4.018 15.509 723 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.54 % Allowed : 14.29 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.33), residues: 670 helix: 0.84 (0.37), residues: 211 sheet: -2.13 (0.48), residues: 90 loop : -0.09 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.002 0.000 HIS A 196 PHE 0.032 0.001 PHE A 266 TYR 0.011 0.001 TYR A 431 ARG 0.001 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.02731 ( 169) hydrogen bonds : angle 4.97692 ( 510) SS BOND : bond 0.00221 ( 15) SS BOND : angle 0.48935 ( 30) covalent geometry : bond 0.00256 ( 5288) covalent geometry : angle 0.49819 ( 7143) *********************** 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 20 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.628 Fit side-chains REVERT: A 306 MET cc_start: 0.8901 (tpt) cc_final: 0.8549 (tpt) REVERT: A 626 MET cc_start: 0.8264 (mmm) cc_final: 0.7717 (tpp) REVERT: A 684 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7823 (pp20) outliers start: 3 outliers final: 3 residues processed: 20 average time/residue: 1.2567 time to fit residues: 26.9434 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 : 0.620 ------------------------------------------------------------------------------- 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 64 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.060098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.048665 restraints weight = 18856.369| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.33 r_work: 0.2783 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5303 Z= 0.096 Angle : 0.497 11.751 7173 Z= 0.252 Chirality : 0.040 0.123 780 Planarity : 0.003 0.026 933 Dihedral : 3.928 16.500 723 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.54 % Allowed : 14.29 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.33), residues: 670 helix: 0.92 (0.37), residues: 211 sheet: -2.04 (0.49), residues: 90 loop : -0.08 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.002 0.000 HIS A 196 PHE 0.010 0.001 PHE A 645 TYR 0.010 0.001 TYR A 431 ARG 0.002 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.02598 ( 169) hydrogen bonds : angle 4.94461 ( 510) SS BOND : bond 0.00196 ( 15) SS BOND : angle 0.46180 ( 30) covalent geometry : bond 0.00222 ( 5288) covalent geometry : angle 0.49685 ( 7143) *********************** 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 19 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.574 Fit side-chains REVERT: A 306 MET cc_start: 0.8969 (tpt) cc_final: 0.8627 (tpt) REVERT: A 413 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8650 (mt-10) REVERT: A 626 MET cc_start: 0.8165 (mmm) cc_final: 0.7675 (tpp) REVERT: A 684 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7776 (pp20) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 1.3035 time to fit residues: 26.5132 Evaluate side-chains 18 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR 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 10 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.0020 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.058053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.046523 restraints weight = 19312.792| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 4.31 r_work: 0.2733 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5303 Z= 0.183 Angle : 0.551 11.966 7173 Z= 0.285 Chirality : 0.041 0.120 780 Planarity : 0.003 0.025 933 Dihedral : 4.211 16.467 723 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.33), residues: 670 helix: 0.93 (0.37), residues: 211 sheet: -2.12 (0.48), residues: 90 loop : 0.01 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 347 HIS 0.003 0.001 HIS A 196 PHE 0.037 0.001 PHE A 266 TYR 0.010 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 169) hydrogen bonds : angle 5.08835 ( 510) SS BOND : bond 0.00302 ( 15) SS BOND : angle 0.55548 ( 30) covalent geometry : bond 0.00418 ( 5288) covalent geometry : angle 0.55115 ( 7143) ********************** 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 : 0.622 Fit side-chains REVERT: A 376 GLU cc_start: 0.8895 (mp0) cc_final: 0.8527 (tt0) REVERT: A 413 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8663 (mt-10) REVERT: A 626 MET cc_start: 0.8160 (mmm) cc_final: 0.7717 (tpp) REVERT: A 684 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7907 (pp20) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 1.4254 time to fit residues: 28.8515 Evaluate side-chains 18 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR 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 15 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.058690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.047164 restraints weight = 19369.846| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.36 r_work: 0.2760 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5303 Z= 0.126 Angle : 0.521 12.114 7173 Z= 0.268 Chirality : 0.040 0.124 780 Planarity : 0.003 0.026 933 Dihedral : 4.113 16.206 723 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.07 % Allowed : 14.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.33), residues: 670 helix: 0.99 (0.37), residues: 211 sheet: -2.08 (0.49), residues: 90 loop : 0.05 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 347 HIS 0.002 0.000 HIS A 196 PHE 0.009 0.001 PHE A 645 TYR 0.010 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.02794 ( 169) hydrogen bonds : angle 5.03186 ( 510) SS BOND : bond 0.00247 ( 15) SS BOND : angle 0.51093 ( 30) covalent geometry : bond 0.00294 ( 5288) covalent geometry : angle 0.52145 ( 7143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3081.43 seconds wall clock time: 55 minutes 11.75 seconds (3311.75 seconds total)