Starting phenix.real_space_refine on Fri Dec 27 13:59:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fei_29028/12_2024/8fei_29028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fei_29028/12_2024/8fei_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_29028/12_2024/8fei_29028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fei_29028/12_2024/8fei_29028.map" model { file = "/net/cci-nas-00/data/ceres_data/8fei_29028/12_2024/8fei_29028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fei_29028/12_2024/8fei_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.20, per 1000 atoms: 0.81 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: 1.16 Conformation dependent library (CDL) restraints added in 629.3 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: 0.73 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: 1.83 Time building geometry restraints manager: 1.41 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.400 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.280 ------------------------------------------------------------------------------- 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 5288 Z= 0.433 Angle : 0.914 9.190 7143 Z= 0.605 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 *********************** 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 : 0.629 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: 1.7619 time to fit residues: 66.2702 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 : 0.630 ------------------------------------------------------------------------------- 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: 4.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.006 0.036 5288 Z= 0.350 Angle : 0.618 6.093 7143 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 *********************** 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 : 0.581 Fit side-chains REVERT: A 306 MET cc_start: 0.8680 (ttm) cc_final: 0.8442 (tpt) REVERT: A 684 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7716 (pp20) outliers start: 7 outliers final: 1 residues processed: 25 average time/residue: 1.2070 time to fit residues: 32.2421 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 : 0.613 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5288 Z= 0.185 Angle : 0.507 7.708 7143 Z= 0.269 Chirality : 0.040 0.139 780 Planarity : 0.003 0.029 933 Dihedral : 4.404 16.698 723 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.07 % Allowed : 10.71 % 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: -1.33 (0.29), residues: 670 helix: -0.49 (0.32), residues: 211 sheet: -2.56 (0.45), residues: 84 loop : -0.59 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.002 0.000 HIS A 196 PHE 0.008 0.001 PHE A 645 TYR 0.010 0.001 TYR A 431 ARG 0.003 0.000 ARG A 497 *********************** 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 26 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.679 Fit side-chains REVERT: A 306 MET cc_start: 0.8641 (ttm) cc_final: 0.8411 (tpt) REVERT: A 684 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7687 (pp20) outliers start: 6 outliers final: 1 residues processed: 24 average time/residue: 1.6217 time to fit residues: 41.4061 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 : 1.314 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.0980 chunk 6 optimal weight: 0.0470 chunk 29 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5288 Z= 0.133 Angle : 0.467 7.465 7143 Z= 0.248 Chirality : 0.039 0.117 780 Planarity : 0.003 0.027 933 Dihedral : 4.109 16.183 723 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.07 % Allowed : 10.71 % 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: -0.87 (0.31), residues: 670 helix: 0.12 (0.35), residues: 211 sheet: -2.38 (0.47), residues: 84 loop : -0.44 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 264 HIS 0.002 0.000 HIS A 196 PHE 0.023 0.001 PHE A 266 TYR 0.009 0.001 TYR A 431 ARG 0.002 0.000 ARG A 497 *********************** 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: 6 poor density : 19 time to evaluate : 0.949 Fit side-chains REVERT: A 306 MET cc_start: 0.8629 (ttm) cc_final: 0.8311 (tpt) REVERT: A 684 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7636 (pp20) outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 1.8667 time to fit residues: 49.1412 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 : 0.688 ------------------------------------------------------------------------------- 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 48 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 58 optimal weight: 0.1980 chunk 16 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5288 Z= 0.270 Angle : 0.541 8.257 7143 Z= 0.284 Chirality : 0.042 0.130 780 Planarity : 0.003 0.026 933 Dihedral : 4.280 16.259 723 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.89 % Allowed : 12.68 % Favored : 86.43 % 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: -0.55 (0.32), residues: 670 helix: 0.45 (0.36), residues: 212 sheet: -2.35 (0.47), residues: 84 loop : -0.25 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 347 HIS 0.002 0.001 HIS A 196 PHE 0.008 0.001 PHE A 628 TYR 0.012 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 *********************** 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 : 0.655 Fit side-chains REVERT: A 306 MET cc_start: 0.8671 (ttm) cc_final: 0.8327 (tpt) REVERT: A 626 MET cc_start: 0.8107 (mmm) cc_final: 0.7575 (tpp) REVERT: A 684 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7790 (pp20) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 1.3676 time to fit residues: 32.1038 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 : 0.768 ------------------------------------------------------------------------------- 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 15 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5288 Z= 0.240 Angle : 0.514 9.103 7143 Z= 0.270 Chirality : 0.041 0.120 780 Planarity : 0.003 0.027 933 Dihedral : 4.266 16.121 723 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.43 % Allowed : 13.04 % Favored : 85.54 % 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: -0.40 (0.32), residues: 670 helix: 0.63 (0.36), residues: 211 sheet: -2.31 (0.47), residues: 84 loop : -0.18 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 347 HIS 0.002 0.000 HIS A 196 PHE 0.027 0.001 PHE A 266 TYR 0.012 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 *********************** 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 25 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.666 Fit side-chains REVERT: A 306 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8403 (tpt) REVERT: A 626 MET cc_start: 0.8042 (mmm) cc_final: 0.7274 (tpp) REVERT: A 684 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7802 (pp20) outliers start: 8 outliers final: 4 residues processed: 24 average time/residue: 1.3204 time to fit residues: 33.8556 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 : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 306 MET 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 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5288 Z= 0.129 Angle : 0.485 10.448 7143 Z= 0.250 Chirality : 0.040 0.123 780 Planarity : 0.003 0.026 933 Dihedral : 4.019 15.438 723 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.07 % Allowed : 13.57 % 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 (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: 0.77 (0.37), residues: 211 sheet: -2.25 (0.46), residues: 90 loop : -0.13 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.002 0.001 HIS A 196 PHE 0.010 0.001 PHE A 645 TYR 0.011 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 *********************** 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: 6 poor density : 18 time to evaluate : 0.555 Fit side-chains REVERT: A 306 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8253 (tpt) REVERT: A 626 MET cc_start: 0.8005 (mmm) cc_final: 0.7264 (tpp) REVERT: A 684 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7749 (pp20) outliers start: 6 outliers final: 3 residues processed: 23 average time/residue: 1.3265 time to fit residues: 32.6720 Evaluate side-chains 21 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 306 MET 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 43 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5288 Z= 0.131 Angle : 0.491 11.145 7143 Z= 0.249 Chirality : 0.039 0.121 780 Planarity : 0.003 0.026 933 Dihedral : 3.930 15.718 723 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.25 % Allowed : 13.93 % 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: -0.23 (0.32), residues: 670 helix: 0.89 (0.37), residues: 211 sheet: -2.20 (0.47), residues: 93 loop : -0.09 (0.33), residues: 366 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 *********************** 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 23 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.565 Fit side-chains REVERT: A 306 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8227 (tpt) REVERT: A 413 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8258 (mt-10) REVERT: A 626 MET cc_start: 0.8000 (mmm) cc_final: 0.7320 (tpp) REVERT: A 684 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7747 (pp20) outliers start: 7 outliers final: 3 residues processed: 21 average time/residue: 1.3251 time to fit residues: 29.7486 Evaluate side-chains 20 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 306 MET 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 18 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5288 Z= 0.136 Angle : 0.495 11.650 7143 Z= 0.252 Chirality : 0.040 0.123 780 Planarity : 0.003 0.026 933 Dihedral : 3.890 15.335 723 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.89 % Allowed : 14.46 % 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: -0.13 (0.33), residues: 670 helix: 0.98 (0.37), residues: 211 sheet: -2.14 (0.48), residues: 93 loop : -0.03 (0.33), residues: 366 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 0.009 0.001 PHE A 645 TYR 0.010 0.001 TYR A 431 ARG 0.001 0.000 ARG A 460 *********************** 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 21 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.643 Fit side-chains REVERT: A 204 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8447 (p0) REVERT: A 306 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8225 (tpt) REVERT: A 413 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8265 (mt-10) REVERT: A 626 MET cc_start: 0.7961 (mmm) cc_final: 0.7333 (tpp) REVERT: A 684 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7767 (pp20) outliers start: 5 outliers final: 3 residues processed: 20 average time/residue: 1.4182 time to fit residues: 30.2331 Evaluate side-chains 21 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 306 MET 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 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5288 Z= 0.200 Angle : 0.524 12.084 7143 Z= 0.267 Chirality : 0.041 0.119 780 Planarity : 0.003 0.026 933 Dihedral : 4.039 15.763 723 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.07 % Allowed : 14.29 % 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: -0.03 (0.33), residues: 670 helix: 1.03 (0.37), residues: 211 sheet: -2.15 (0.48), residues: 93 loop : 0.07 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 347 HIS 0.002 0.001 HIS A 196 PHE 0.036 0.001 PHE A 266 TYR 0.010 0.001 TYR A 431 ARG 0.002 0.000 ARG A 460 ********************** 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 22 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.628 Fit side-chains REVERT: A 204 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8408 (p0) REVERT: A 306 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8414 (tpt) REVERT: A 413 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 626 MET cc_start: 0.7805 (mmm) cc_final: 0.7266 (tpp) REVERT: A 684 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7864 (pp20) outliers start: 6 outliers final: 4 residues processed: 20 average time/residue: 1.2964 time to fit residues: 27.7262 Evaluate side-chains 22 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 331 MET 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 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.059896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048490 restraints weight = 18839.732| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 4.31 r_work: 0.2788 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5288 Z= 0.144 Angle : 0.497 12.187 7143 Z= 0.255 Chirality : 0.040 0.115 780 Planarity : 0.003 0.026 933 Dihedral : 3.940 15.337 723 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.07 % Allowed : 14.29 % 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: 0.00 (0.33), residues: 670 helix: 1.08 (0.37), residues: 211 sheet: -2.13 (0.48), residues: 93 loop : 0.08 (0.34), residues: 366 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 0.009 0.001 PHE A 645 TYR 0.011 0.001 TYR A 431 ARG 0.001 0.000 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1737.61 seconds wall clock time: 33 minutes 44.69 seconds (2024.69 seconds total)